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Biointerpreter User Manual #259, 4th Cross, “Apurva Buildings”, 80

Contents

1. 45 Genetypsc genomics simplified Biointerpreter User Manual Gene list for Selected Cancer Gene Expression Description Click on Unigene to view detail annotation of the gene si Gene Blood Bone Gene Name Symbol Tumor Tumor Hs 171695 Hs 171695 pusp DU specificity yp phosphatase 1 Hs 1908 proi Proteoglycan 1 up up secretory granule Filamin A alpha actin binding Up protein 280 Hs 250899 Hs 250899 HSBP1 op ES eroaa cell Hs 25155 Hs 25155 NET1 transforming gene Up 1 Glucosidase beta Hs 282997 Hs 282997 GBA acid includes Up glucosylceramidase List of genes which are differentially regulated in the selected cancer type will be displayed in result window The type of regulation Up or down for the gene under the specific cancer type will be given In the above figure for Hs 171695 under Blood tumor the result is Up It specifies Hs 171695 is up regulated in blood tumor Note indicates no data available for the gene under the cancer type To view the genes which are differentially regulated in all the selected cancer types i Select the cancer types ii Select AND radio button at the bottom iii Click the Table View button Genes which are differentially regulated in all the selected cancer types will be displayed in the result window 46 Genetypsc genomics simplified Biointerpreter User Manual To view the Pie Chart iv
2. Genetypsc genomics simplified Gene Name GeneOntologyID GeneOntologyName GO 0005 3 GO 0005634 SH3 domain binding glutamic acid rich protein like cytoplasm C nucleus C Hs 124503 Hs 124503 TCF8 nucleus C nucleus C 49 Biointerpreter User Manual Link in the Unigene ID column will lead the detailed annotation for the gene Biointerpreter has comprehensive frequently updated annotation for the genes Gene Ontology ID is linked to corresponding gene ontology in Gene ontology website Similarly we can get the genes which are associated with any one of the selected pathways a Select the Gene ontology by clicking on the corresponding check box b Select the OR radio button at the bottom c Click the Table View button Biointerpreter displays the genes which are associated with any one of the selected gene ontology on result window To view the Pie Chart for the selected pathways iii Select the Gene Ontology iv Click the Pie Chart button Biointerpreter displays the pie chart on result window cytoplasm C 1660 nucleus C 4119 50 Genetypsc genomics simplified Biointerpreter User Manual Protein Domain No of P value Domain genes E Immunoglobulin C 2 Typel153 OO 2 3 Kazal type serine protease inhibitors 1E 09 37 E Homeodomain 192 1E 09 ATPases associated with a variety 1E 09 of cellular act i
3. Biointerpreter User Manual Unigene Gene Gene Chromosome Cytoband Lii ID Symbol Name SH3 domain binding Hs 108029 Hs 108029 SH3BGRL glutamic x acid rich protein like Filamin A Hs 195464 Hs 195464 FLNA Pha actin binding protein 280 Methyl CpG binding Hs 200716 Hs 200716 MECP protein 2 x xq28 Rett syndrome x Midline 1 Hs 27695 Hs 27695 MID1 Opitz BBB y Xp22 syndrome PRAL Hs 29595 Hs 29595 PRAF2 domain family member 2 S100 Hs 2962 Hs 2962 S100P calcium binding protein P Spondin 2 extracellular 4 4016 3 Hs 302963 Hs 302963 _SPON2 To view the pie chart for the selected Chromosome i Select the Chromosome ii Click the Pie chart button ChromosomeName 4 883 X 906 Biointerpreter displays the pie chart in the result window 34 Genetypsc genomics simplified Biointerpreter User Manual Diseases Diseases No of Disease P value genes E faias O O o o f eo E fanai cancers O r eo Efans o o a f eo E farns o o o j eo E faspergnosistr 1 mo E fasma o e i eo E praader cancer s mo E foreast cancerto23 mo E cervical cancertsog s mo Chronic Obstructive Pulmonary Disease 80 E cockayne Syndromeli2 o Colon Cancer 654 1E 09 Select All Clear And Or Default TableView Pie Chart Biointerpreter finds list of the significant disease for the query list in the above format 1 Disease ii
4. Pathway Comp i nd coaaulati acscade ag and coagulation cascades 1E 09 69 P value by chi square test Glyoxylate and dicarboxylate metabolism 14 1E 09 1E 09 Natural killer cell mediated cytotoxicity 133 fay beta Alanine metabolism 24 1E 09 A Limonene and pinene degradation 29 2 ae 09 E Butanoate metabolism 44 4 15609 E Propanoate metabolismi 2 1o E Glycerolipid metabolism 62 3 1509 E Tryptophan meteboismies 3 109 E Histidine metabolism 42 2 Valine leucine and isoleucine degradation 52 1E 09 Select All Clear And Or Default Tableview go Logical query Select pie chart to view the AND genes in all the selected pathway Select table view to view genes Graphical representation of OR genes in any one of the selected pathway in the selected pathway the selected pathways 14 Genetypsc genomics simplified Biointerpreter User Manual The details 1 Check box to select the pathways and then to view the genes associated with the pathways User can select a pathway and view the genes associated with that particular pathway Pathway P value is the short term for Probability value 3 It tells us about the probability of getting significant result from your list when compared to population Chi square test has been used to calculate the P value Chi square is a common statistical method used to compare the observed data and expected data Usu
5. Arthritis Gout and pseudogout Still s disease Ankylosing spondylitis joint inflammation inflammation of joint Aspergillus Aspergillosis Asthma wheezing wheezy status asthmaticus bronchospasm gt asthmatic Spielmeyer Vogt Sjogren Batten disease Curschmann batten Steinert syndrome Batten s syndrome Gibb syndrome Rossolimo Steinert myotinic dystrophy Congenital myotonic dystrophy dystrophia myotonica myotonia dystrophica Bladder Cancer transitional cell carcinoma bladder carcinoma Blastomycosis Chicago Disease Gilchrist s disease Bone Cancer Osteosarcoma Malignant Fibrous Histiocytoma Hyaline Brain Tumor intracranial tumor ganglioglioma disembryoplastic neuroepithelial tumor oligoastrocytoma oligodendroglioma Breast carcinoma Mammary cancer breast cancer mammary carcinoma breast tumor Canavan ACY2 Deficiency ASP Deficiency ASPA Deficiency Aminoacylase 2 Deficiency Aspartoacylase Deficiency Bertrand Disease Spongy Degeneration of the Central Nervous System Van Bogaert Bertrand Syndrome 70 Genetypsc genomics simplified Biointerpreter User Manual Cervical Cancer Cervical cancer cervix tumor cervical carcinoma Chagas Disease Chagas Disease Trypanosoma cruzi Schizotrypanum cruzi American trypanosomiasis Chickenpox Chicken pox Varicella VZV chickenpox Cholera Cholera Vibrio cholerae Chronic Chronic obstruct
6. The list of genes associated with selected gene ontology will be displayed at result window with the following information Query ID Unigene ID with link to detailed annotation Gene Name Gene symbol Gene Ontology ID GO ID with link to Gene Ontology database Gene ontology Name 48 Genetypsc genomics simplified Biointerpreter User Manual Biointerpreter allows you to find genes which are associated with all the selected Gene ontology Here is how a Select the Gene ontology by clicking on the corresponding check boxes b Select the AND radio button c Click the Table View button Gene Ontology Gene No of Ontology genes P value nucleus C 4119 cytoplasm C 36607 1E 09 a plasma membrane Ote f o f eoo 3 iw unfolded protein binding LSI 3 10s Sifextracetular region cte671 9 1o Select All And amp Or Default Tableview Pie Chart In the above figure the user has selected nucleus and cytoplasm We can get the genes which are involved in both the Gene ontology by clicking on the table view Refer the table given below Un T Gene dbe Symbol Hs 108029Hs 108029 SHSBGRL Peptidylprolyl GO 0005 3 Hs 110364 Hs 110364 PPIC isomerase C cytoplasm C cyclophilin C GO 0005634 GO 0005737 S100 calcium aaa nucleus C Hs 112408 Hs 112408 S100A7 binding protein A7 cytoplasm C Transcription factor GO 0005634 8 represses interleukin 2 expression
7. hypoglycemia end stage renal disease ESRD type 2 DM hyperosmolar nonketotic syndrome HHNS HNKS retinopathy metabolic syndrome syndrome X Diabetes Mellitus ketosis prone diabetes autoimmune diabetes mellitus brittle Typet diabetes mellitus diabetic ketoacidosis DKA maturity onset diabetes MODY gestational diabetes mellitus GDM chamber pot dropsy latent autoimmune diabetes of the adult LADA diabetes mellitus type1 Diphtheria Diphtheria Dyspepsia indigestion dyspepsia stomach upset upset stomach Ebola Ebola fever Filoviridae Haemorrhagic Fever 71 Genetypsc genomics simplified Biointerpreter User Manual Endometrial Endometrial Cancer endometrial carcinoma Cancer Fever fever febrility febricity pyrexia pyrogen pyrogenic feverish Fibrosis Fibros Myelofibrosis fibrosis fibrocystic disease of the pancreas mucoviscidosis Filariasis Filariasis Wuchereria bancrofti Brugia malayi Brugia timori elephantiasis filaria Gastroenteritis gastroenteritis rotavirus Giardiasis Giardiasis beaver fever Giardia lamblia Glaucoma glaucoma intraocular pressure optic nerve damage Goodpasture S Goodpasture pulmonary haemorrhage syndrome interstitial Syndrome nephritis pneumorenal syndrome _ glomerulonephritis renopulmonal syndrome Graves Disease Grave goiter hyperthyroidism thyrotoxicosis Flajani Basedow Marsh Par
8. GeneRIF Displays the concise phrase describing a function or functions curated from published scientific articles 1 a concise phrase describing a function or functions 2 A published paper describing that function implemented by supplying the PubMed ID of a citation in PubMed Link to GeneRIF Gene Summary Displays the descriptive text about the gene its cellular localization its function and its effect on phenotype Gene Ontology Describes gene products in terms of their associated biological processes cellular components and molecular functions in a species independent manner GO ID will leads to the corresponding gene ontology term description in the Gene Ontology website Protein Ontology Describes proteins in terms of their associated biological processes cellular components and molecular functions in a species independent manner This data was retrieved from Swissprot 65 Genetypsc genomics simplified Biointerpreter User Manual Protein Function General description of the function s of a protein as derived from Swissprot Keyword The keyword is a subject reference which provides information that can be used to generate indexes of the protein entries based on functional structural or other categories as derived from Swissprot Kegg Pathway KEGG PATHWAY is a collection of manually drawn pathway maps representing molecular interactions and reaction networks for metabolism human diseases cellular proces
9. 0 0002 l 0 0009 28 0 0013 3 0 0151 3 0 0162 0 0309 19 6 1173 14 683 21 296 2 x 906 6 2 1481 11 11 1368 10 10 892 Fi 12 1128 18 335 3 22 530 4 4 20 590 Select All Clear And Or Default TableView Pie Chart l i Biointerpreter generates the list of the chromosomes for the genes in your query 1 Chromosome ii Number of genes present in the chromosome in the query list iii P value The number in the square bracket specifies the number of genes present in the chromosome ey Genetypsc genomics simplified Biointerpreter User Manual To view the genes present in a Chromosome i Select the Chromosome by clicking the corresponding check box ii Click the Table View button Chromosome No of genes P value Chromosome 1 2263 19 5 969 10 1E 09 6 1173 8 IE O i apos n o 14 683 21 296 e E 1018921 lt 4 883 5 1 Select All Clear S And Or Default Tableview Pie Chart 1E 09 In the above figure the user would like to view the genes present in Chromosome 4 and X Biointerpreter finds the genes present in the chromosome 4 and X and reports in the result window The list of genes present in the selected chromosome will be displayed at the result window with the following information Query ID Unigene ID with link to detailed annotation Gene Name Gene symbol Chromosome Cytoband 33 Genetypsc genomics simplified
10. 110364 pprc PePptidylprolyl isomerase C cyclophilin C Hs 112408 Hs 112408 1007 9200 calcium binding protein A Hs 128316 Hs 128516 BAIAP BAI1 associated protei 40 B Genetypsc Biointerpreter User Manual Number of related keywords found in the comprehensive annotation of the gene is displayed under Cytoplasm and integral to membrane This number is hyperlinked to get detailed annotation of the gene Related keywords for the Cytoplasm and integral to membrane will be highlighted in the detailed annotation For example in the above figure 2 related keywords of Cytoplasm were found in Hs 108029 1 related keywords of Integral to membrane were found in Hs 109225 To view genes localized in any one of the selected sub cellular location i Select the sub cellular localization by clicking on the corresponding check boxes ii Select OR radio button at the bottom iii Click the Table View button List of genes localized in any one of the sub cellular localization will be displayed at result window To view the pie chart for the selected sub cellular localization i Select the sub cellular localization ii Click the Pie chart button Biointerpreter displays the pie chart at the right hand page Chart Extracellular 1332 Cytoplasm 802 LocalisationName Cytoplasm 3802 Extracellular 1332 The number in the square bracket specifies the number of genes localized i
11. 122 Epidermal growth factor like i B R al Fibronectin type 3 domaim 150 1E 09 Dual specificity phosphatase 1E 09 catalytic domain 24 E Calcium binding EGF like domain 69 5 16 09 al Methyl CpG binding domain 8 a 1E 09 Histone H2B 17 1E 09 Select All Clear And Or Default Tableview Pie Chart Biointerpreter gives you list of significant protein domains with number of genes Supporting the protein domain in the query list Number within the square bracket with protein domain specifies the number of genes supporting the protein domain in the genome To view the genes involved in the particular protein domain ii Select the Domain by clicking on the corresponding check box iii Click the Table View button The list of genes associated with the selected protein domain will be displayed at result window with the following information Query ID Unigene ID with link to detailed annotation Gene Name Gene symbol Protein domain ID SMART ID with link to SMART database Protein domain Biointerpreter allows you to find genes which are associated with all the selected Protein domains Here is how 51 Genetypsc genomics simplified Biointerpreter User Manual a Select the Protein Domain by clicking on the corresponding check boxes b Select the AND radio button c Click the Table View button Protein Domain No of genes P value Domain Ei immunoglobulin C
12. Default Chromosome No of genes P value e ema O ooo oe o o e a e S E Cema o O o m hesa f o Oo e E kosa f o f O o E psss ts l l i i Genetypsc genomics simplified Result Window Back New Search intr Bottom of the table Detail Annotation Gene list for Selected Pathways Description Click on Unigene to view detail annotation of the gene ee waging Gene Gene vee ec Symbol Name hsa04110 CCNE1_HUMAN Hs 244723 CCNE1 Cyclin E1 Cell cycle Cyclin dependent hsa04110 hsa05218 kinase 7m Cell cycle inhibitor Melanoma 1A p21 Cip1 PathwayID PathwayName CONTA _HUMANHs 3 70771 CDKN1A Table View Biointerpreter Detailed Annotation Description Detailed Annotation For Hs 244723 Gene Symbol CCNE1 SwissPort ID CCNE1 HUMAN Unigene ID IHs 244723 Activation Apoptosis Cell Cycle Cell Differenti Machinery Gene Regulation Inflammation Met Breast Cancer 2 Oncogenesis 1 Prognosis 1 Transcription Regulation 1 Transcription Proliferation 5 Cell Differentiation 1 Gene F Regulators 2 Inflammation 1 Lymphoma 1 Machinery 5 Functional Annotation Genotypic Curation Stimulated response Signal transduction Grow Gene Expression Data response Cell specific expression Cell different Growth Factor Studies Other Infection Viral Tr 10 Biointerpreter User Manual Summary Report Summary report gives the following details Study Name The s
13. Factor None None Up 1 None cholinergic differentiation factor V fos FBJ murine osteosarcoma viral oncogene homolog Hs 2564 Hs 25647 In the above figure for Hs 19192 under metabolism condition the result is Up 1 It specifies that Hs 19192 is up regulated in metabolism 23 Genetypsc genomics simplified Biointerpreter User Manual Note None indicates no data available for the gene under the particular gene expression condition To view the gene expression data in detail click on Up 1 you will get the following gene expression details at the bottom of the page Unigene ID Linked to Unigene PMID Article s Pubmed ID from which the data has been curated PMID is linked to corresponding article in Pubmed Experiment Experiment details Condition Condition in which the genes are expressed Regulation Type of regulation PMID Genes up regulated in human hepatoma cells by a liver Hs 1919 2 11834723 HNF4alpha_metabolism specific transcription factor Hepatocyte nuclear factor 4 HNF 4 alpha To view the genes which are differentially regulated in all the gene expression conditions i Select all the gene expression conditions ii Select OR radio button at the bottom iii Click the Table View button Expression Condition P value Atherosclerosis 164 Gene Activation response 1285 Inflammation 250 ca Gle 77 CEESESE ooo Response to organic compunds 34
14. Hs 120759 Apop Popoprotein B induding Ag x system antigen l phenotype Transcription factor 8 represses Hs 124503 Hs 124503 cardiovascular system phenotype e TE eme craniofacial Hs 133397 Hs 133397 ITGA6 Integrin alpha 6 phenotype craniofacial MP 0005385 phenotype Hs 136348 Hs 136348 POSTN Periostin osteoblast specific factor cardiovascular system phenotype interleukin 2 expression Link in the Unigene ID column will lead the detailed annotation for the gene Biointerpreter has comprehensive frequently updated annotation for the genes Phenotype ID is linked to corresponding phenotype in the Mammalian phenotype browser Similarly we can get the genes which are associated with any one of the selected Phenotype i Select the Phenotype by clicking on the corresponding check box ii Select the OR radio button at the bottom iii Click the Table View button Biointerpreter displays the genes which are associated with any one of the selected phenotype on result window To view the Pie Chart for the selected Phenotype i Select the phenotype ii Click the Pie Chart button Biointerpreter displays the pie chart on result window 63 Genetypsc genomics simplified Biointerpreter User Manual digestive alimentary phenotype 493 cardiovascular system phenot Chart craniofacial phenotype 417 PhenotypeName cardiovascular system phenotype 919 crariof
15. Number of genes involved in the function in the query list iii P value The number in the square bracket specifies the number of genes involved in the disease in the genome To view the genes involved in a disease i Select the Disease by clicking the corresponding check box ii Click the Table View button Biointerpreter will display the genes involved in the particular disease in the result window with the following information e Query ID e Unigene ID with link to detailed annotation e Gene Name 35 B Genetypsc Biointerpreter User Manual e Gene symbol e List of possible diseases To view genes involved in all the selected Diseases a Select the disease by clicking on the corresponding check boxes b Select AND radio button at the bottom c Click the Table View button Diseases No of Disease P value genes E nass o O eo E anai cance OO O r w Epam oo o S w E farriss j o w E faspergnosss 1 wo Ehsan O e S w e se Breast Cancer 923 1E 09 Select All Clear And Or Default TableView Pie Chart In the above figure the user would like to view the genes involved in Bladder cancer breast cancer Biointerpreter finds the genes involved in both of the disease and reports in the result window 36 Genetypsc genomics simplified Biointerpreter User Manual Unigene Gene Bladder Breast a ID Symbol ENE Tamne Cancer Cancer Hs 109225 Hs 10
16. Prometaphase Meta Phase Metaphase M Phase Inter Phase Interphase G2 Phase G1 Phase Cyclin Dependant Checkpoint Cell Division Cycle Cell Cycle Cdk Anaphase Cell Totipotent Stem Cells Stem Cell Somatic Cell Pluripotent Differentiation Lineage Germ Cell Cell Differentiation Cell Division Meiosis Mitotic Mitosis Mitogen Meiotic Cytokinesis Fission Dividing Cell Daughter Cells Cellular Division Cell Division Budding Cell Migration Cellular Movement Cell Spreading Cell Movement Cell Motility Cell Migration Cell Spindle Positioning Polarity Morphogenesis Cell Size Cell Morphogenesis Shape Cell Patterning Biogenesis Cell Plasticity Plasticity Cell Proliferation Proliferation Proliferating Cellular Trafficking Traffic Cellular Transport Trafficking Chemotaxis Chemotaxis Chemotaxin Chemotactic Chemotaxic Chemotactin Chemoattractant Chromosomal Meiosis Kinetochore Centromere Tubulin Sister Chromatid Segregation Separin Securin Motor Protein Monopolin Microtubules Condensin Cohesion Cohesin Chromosome Segregation Chromosomal Segregation Complement Opsonisation Complement Coagulation Complement Activation Activation Classical Pathway Alternative Pathway 67 Genetypsc genomics simplified Biointerpreter User Manual Degeneration Degenerative Degeneration Degenerate Degeneracy Dna Machinery Re
17. Tableview Pie Chart Up Biointerpreter generates the drug response results in the above format i Drug Type of drug treatment ii Up Number of up regulated genes in the query list in the corresponding drug response condition iii Down Number of down regulated genes in the query list in the corresponding drug response condition iv Both Number of genes which are up and down regulated in the corresponding drug response condition v P value Number in the square bracket specifies number of genes in the database differentially regulated for the corresponding drug response condition 26 Genetypsc genomics simplified Biointerpreter User Manual To view the genes which are differentially regulated for the particular drug response condition i Select the Drug response condition ii Click on the Table View button P value pa fia oo an Cancer drug resistance 203 a o o 0 0004 an Response to Cancer Drugs 928 7 13 9 1609 Response to Other Drugs 1156 10 16 o 1609 Cancer drug treatment 1594 E brug treatments 7 2 a0 Select All Clear And Or TableView Pie Chart Up List of genes which are differentially regulated in the selected drug response conditions will be displayed in the result window Each gene is supported by the type of regulation with number of sub conditions available for the particular gene expression condition Description Click
18. View button Biointerpreter will display the genes localized in the particular sub cellular localization in the result window with the following information Query ID Unigene ID with link to detailed annotation Gene Name Gene symbol All possible Sub cellular locations 39 Genetypsc genomics simplified Biointerpreter User Manual To view genes localized in all the selected sub cellular location i Select the sub cellular localization by clicking on the corresponding check boxes ii Select AND radio button at the bottom iii Click the Table View button Cellular Localization No of genes P value an Endoplasmic Reticulum 754 9 1609 E fexraceluiartizaa f s eoo E nucieust49es a eo an Plasma Membrane 20972 E Secreted 1397 a a E 19 Localization Lysosomes 228 0 001 Centrosome 130 Golgi Apparatus 761 Integral to membrane 3451 Select All Clear E And r Or Default TablevView Pie Chart In the above figure the user would like to view the genes localized in both Cytoplasm and Integral to membrane Biointerpreter finds the genes localized in both the cytoplasm and integral to membrane and report in the result window Integral Gene Name Cytoplasm to membrane Unigene Gene Query id ID Symbol SH3 domain binding Hs 108029 Hs 108029 SH3BGRL glutamic acid rich protein 0 Hs 109225 Hs 109225 vcami Vascular cell adhesion ae IS molecule 1 Hs 110364 Hs
19. actin er ae Hs 118400 Hs 118400 FSCN1 protein Strongylocentrotus purpuratus ete ol agrea ATP binding cassette sub family Ss oo Hs 124649 Hs 124649 ABCG1 WHITE member 1 BAIi associated protein 2 Integrin alpha 6 Periostin osteoblast specific factor pe 138860 AREST ET RHGAP Rho GTPase activating protein id 2 amp 24 0 A P et Hs 143250 Tenascin C hexabrachion lt lt Hs 163867 cota CD14 molecule gt z ae Hs DUSP1 Dual specificity phosphatase 1 19 Genetypgc Biointerpreter User Manual Number of related keywords of the function found in the comprehensive annotation of the gene is displayed under each function This number is hyperlinked to get detailed annotation of the gene Related keywords for the function will be highlighted in the detailed annotation For example in the above figure 2 related keywords of Angiogenesis were found in Hs 109225 2 related keywords of Antigen processing and Presentation were found in Hs 111779 If you click on Angiogenesis found in Hs 109225 it will give you detailed annotation for Hs 109225 Detailed Annotation For Hs 111 Highlighted keywords Vegt Endothelial Growth Endothelial Cell Growth Angioporetin Angiogenetic Angiogenesis Angiogen Gene Name Fibroblast growth factor 9 glia activating factor Gene Symbol FGF9 SwissPort ID FGF9 HUMAN Unigene ID Hs 111 Angiogenesis Cell Cycle Cell Differentiation Cell Division Cell Morpho
20. corresponding to the genes in the query Gene Expression Biointerpreter finds the genes which are differentially regulated upon disease experimental conditions Protein Domain A compact structural domain that is found amongst diverse proteins is likely to fold independently within its structural environment Significant protein domains with number of genes supporting the protein domain in the query list Tissue Expression Describes list of the significant tissues in which the query genes expressed Drug Response Describes Genes which are differentially regulated for the particular drug response condition Phenotype The observable physical or biochemical characteristics of an organism as determined by both genetic makeup and environmental influences Describes significant genes involved in the phenotypic change 13 Genetypsc genomics simplified Biointerpreter User Manual Explanation of Results Viewing the Result Categories amp interpretation Pathway The user can view the Pathways related to queried genes in the pathway table The detailed pathway table is displayed as below Biointerpreter finds the list of pathways with number of genes involved in the pathway in the query list and also the corresponding P value Number within the square bracket specifies the number of genes in the pathway of the genome No of genes P value Pathway E Regulation of actin cytoskeletent E cell adhesion moleculesT
21. different parameters like genomic location pathways diseases drug response and so on This makes Biointerpreter a truly comprehensive resource that would definitely work the best for you e Can decipher the significance of a gene list in minutes This saves you enormous amounts of time and effort e Allows you to query using diverse gene identifiers 17 different gene ids like Affymetrix Agilent Genbank Unigene etc Biointerpreter combines the facilities provided by multiple tools using any ID type e Allows you to drill down to the source of information allowing you to quickly validate the reliability of the information e Allows you to switch between organisms at will a unique feature of Biointerpreter For example for a list of mouse genes you can view the biological significance of homologs genes in human database e Helps you to readily identify hot molecules like cancer markers drug targets etc hidden in your list You will not miss important genes that control key processes Biointerpreter Design and Contents Biointerpreter is designed based on Genotypic s more than 6 years experience in microarray analysis services The suggestions and requirements of microarray users worldwide have been translated to a highly efficient user friendly product It contains comprehensive and verified annotations from various sequence and annotation databases Contains microarray data tables from over 500 publications and is constantl
22. gene DOWN by Testosterone 1 estradiol g inhibitors letrozole and anastrozole and an antiestrogen tamoxifen Biointerpreter provides a way to view all the drug response details for a gene To view all the gene expression details of a gene click on the links in the Unigene ID in the above table All gene expression data available for the gene will be presented with the following information Unigene ID Linked to Unigene PMID linked to Pubmed Experiment Condition summary Condition Experimental condition Regulation Type of regulation Major classification Type of drug treatment To view the genes which are differentially regulated in all the selected drug response conditions i Select the drug response conditions ii Select AND radio button at the bottom iii Click the Table View button Genes which are differentially regulated in all the selected drug response conditions will be displayed at the result window 28 Genetypsc genomics simplified Biointerpreter User Manual To view the Pie Chart Select the drug response conditions ll Select the desired regulation type Up Down Both from the pull down menu at the bottom Ill Click the Pie Chart button Cancer drug treatment 1594 Response te Other Drugs MHS Drug treatment 439 Response to Cancer Drugs 928 DrugName Response to Cancer Drugs 928 Response to Other Drugs 1156 Cancer drug treatment 1594
23. genomics simplified Biointerpreter User Manual Lung Cancer Lupus Erythematosus Lyme Disease Lymphoma Malaria Measles Motor disease Myasthenia Gravis Myeloma Obesity neuron Obsessive Compulsive Disorder Ovarian Cancer Pancreatic Cancer Parkinson Disease Pertussis Pick S Disease Plague Pneumonia Poliomyelitis Prion Disease Prognosis amp Diagnosis Prostate Cancer Psoriasis Pus Rabies Reiter S Disease Lung cancer bronchogenic carcinoma bronchoalveolar carcinoma oat cell carcinoma lung carcinoma Lupus erythematosus chronic inflammatory disorder SLE Discoid Lupus erythematosus DLE Lyme Borrelia burgdorferi Tick borne meningopolyneuritis Bujadoux syndrome Bannwarth syndrome sheep tick fever Lymph tissue malignancy lymphoma tumor of the B lymphocytes NHL Malaria ague fever marsh fever Plasmodium Measles rubeola Morbillivirus Koplik motor neuron Myasthenia gravis myeloma Obesity corpulency overweight stoutness adiposis embonpoint obese Janet Psychastenia obessive compulsive disorder Ovarian cancer malignant ovarian neoplasm ovarian carcinoma Pancreatic cancer neuroendocrine tumor pancreatic carcinoma Parkinson Progressive supranuclear palsy Parkinsonism Paleostriatal syndromespasmus agitans pallidal syndrome pallidum syndrome paralysis agitans shaking palsy spasmus agitans paralysis agitans
24. selected pathways i Select the pathway by clicking on the corresponding check box il Select the OR radio button at the bottom iii Click the Table View button Biointerpreter displays the genes which are associated with any one of the selected pathways in the result window To view the Pie Chart for the selected pathways i Select the pathways ii Click the Pie Chart button Biointerpreter displays the pie chart on result window Type diabetes mellitus 44 Antigen processing and presentation 2 Cytokine cytokine receptor interaction 261 Antigen processing and presentation 2 ype I diabetes mellitus 44 ytokine cytokine receptor interaction 261 Number in the square bracket shows the number of genes involved in the pathway in genome 17 Genetypsc genomics simplified Biointerpreter User Manual Function Function No of genes P value E lactivation 4856 1E 09 E fAageingt379 a E angiogenesis 682 1E 09 Antigen Processing And a Presentation 1554 T E fapoptosist20261 1E09 ae E foot anesor a 1 09 I loot onietzery ae aes E cell Differentiation 1363 1E 09 cot oniiontieroy ge aes foot mraos 16 1 09 Biointerpreter finds list of functions that are over represented in query gene list The details are e Function e Number of genes involved in the function in the query The number in the square bracket specifies the number of ge
25. whooping cough pertussis Crocker Farber Niemann Pick Ludwig lipid histiocytosis phosphatidolipoidosis phosphatidosis sphingomyelin lipidosis sphingomyelinosis sphingomyelin reticuloendotheliosis pestilence Yersinia pestis Black Death rat flea Xenopsylla cheopis plague Pneumonia pneumoniae infantile paralysis acute flaccid paralysis AFP polio Prion Kuru Scrapie marker prognosis diagnosis prognostic diagnostic Prostate Cancer adenocarcinoma glandular cancer prostatic intraepithelial neoplasia prostate carcinoma Psoriasis Koebner acanthosis purulence purulency purulent Lyssavirus Rabies Fiesinger Reiter Waelsch arthritic spirochaetosis arthritis dysenterica arthritis urethrica blenorrhagic balantiform keratoderma blenorrhagic idiopathic arthritis conjunctivo urethrosynovial syndrome infectious uroarthritis nongonococcal 73 Genetypsc genomics simplified Biointerpreter User Manual urethritis oculo urethroarticular syndrome polyarthritis enterica polyarthritis urethritica simplex postdysenteric arthritis postdysenteric rheumatoid postdysenteric syndrome Ruhr rheumatism postenteric rheumatoid reactive arthritis sexually acquired reactive arthritis spirochaetosis arthritica uretheal arthritis urethral rheumatism urethro oculo articular syndrome urethro oculosynovial syndrome uroarthritis venereal arth
26. 2 Typel153 na Wi Homeodomain 192 ATPases associated with a variety 4 1E 09 of cellular acti 122 Select All Clear And Or Default TableView Pie Chart In the above figure the user has selected Immunoglobulin and Homeodomain We can get the genes which have both the protein domain by clicking on the table view Refer the table given below Gene list for Selected Protein Domain Description Click on Unigene to view detail annotation of the gene _q Unigene Gene Gene a ee E Query id ID Symbol Name ProteinDomainID ProteinDomainName D Vascular cell SM00408 EEE A A ET Hs 109225 Hs 109225 VCAM1 adhesion se molecule 1 rPe actor SM00389 Hs 124503 Hs 124503 TCF8 represses Homeodomain interleukin 2 expression SM00389 Hs 168586 Hs 168586 TLX2 leukemia Homeodomain homeobox Neuronal cell SM00408 ern Hs 21422 Hs 21422 NRCAM adhesion oe molecule rpe Link in the Unigene ID column will lead the detailed annotation for the gene Biointerpreter has comprehensive frequently updated annotation for the genes ProteinDomain ID is linked to corresponding protein domain in SMART database 52 B Genetypsc Biointerpreter User Manual Similarly we can get the genes which are associated with any one of the selected protein domains i Select the protein domain by clicking on the corresponding check box ii Select the OR radio button at the bottom iii Click the Table View button Bio
27. 5 Ta TRFRRRRRRERR T Myopathy 410 Anti oxidant treatment 447 Normal Vs Cancer 498 Cancer Stages 107 Primary Tumor Vs Metastasis 1847 z i z i m d A Cancer specific 1734 Gene regulation 107 Select All Clear and or Defauk TableView Pie Chart 24 Genetypsc genomics simplified Biointerpreter User Manual Genes which are differentially regulated in all the selected gene expression conditions will be displayed at the result window To view the Pie Chart i Select the gene expression conditions ii Select the desired regulation type Up Down Both from the pull down menu at the bottom iii Click the Pie Chart button Cell Cycle 277 Hormone treatment 970 Gene mutation over expression 1 GeneName Cell Cycle 277 Gene mutation over expression 1 Hormone treatment 970 Number in the square bracket specifies number of genes in the genome differentially regulated for the corresponding gene expression condition 253 Genetypsc genomics simplified Biointerpreter User Manual Drug Response Drug P value El forugresistancetae it x o 0 0001 E ca ncer drug resistance 203 3 o o 0 0004 E response to Cancer orugstozel_ 7 19 9 16 09 E Response to Other Drugs 1156 i0 16 o 16 09 E ca ncer drug treatment 1594 zi 8 7 16 09 E orug treatments 7 gt ieo Select All Clear A And M
28. 9 al Gross deletions 524 Select All Clear And Or Default TableView Pie Chart In the above figure the user has selected Regulatory We can get the genes which have the mutation types by clicking on the table view Refer the table given below 58 Genetypsc genomics simplified Biointerpreter User Manual Gene list for Selected Gene Mutation Description Unigene Gene Query id ID Symbol Gene Name Mutation Apolipoprotein B Hs 120759 Hs 120759 APOB including Ag x Regulatory antigen Hs 163867 Hs 163867 CD14 CD14 molecule o Hs 2030 Hs 2030 THBD Thrombomodulin gt eatory ulatory Leukemia inhibitory factor Hs 2250 Hs 2250 iain ESE differentiation factor Matrix Hs 2256 Hs 2256 MMp7 Metallopeptidase Regulatory 7 matrilysin uterine Matrix metallopeptidase Regulatory 3 stromelysin 1 progelatinase Link in the Unigene ID column will lead the detailed annotation for the gene Biointerpreter has comprehensive frequently updated annotation for the genes Mutation is linked to corresponding gene in Human gene mutation database Similarly we can get the genes which are associated with any one of the selected Mutation 1 Select the mutation by clicking on the corresponding check box 2 Select the OR radio button at the bottom 3 Click the Table View button Biointerpreter displays the genes which are associated with any one of the selected mutation
29. 9225 VCAM1 Vascular cell adhesion molecule 1 Hs 111779 Hs 111779 SPARC Secreted protein acidic cysteine 2 Epes rich osteonectin Hs 112408 Hs 112408 S1i00A7 S100 calcium binding protein A7 0 2 Fascin homolog 1 actin bundling 400 Hs 118400 FSCNi protein Strongylocentrotus purpuratus Hs 120759 Hs 120759 apog APolipoprotein B including Ag x antigen Hs 133397 Hs 133397 ene Integrin alpha 6 i eee Periostin osteoblast specifi ic factor Hs 139389lHs 130389 csre CystatineyM o l3 z oT T Tenascin C hexabrachion Oo 2 Hs 155017 Hs 155017 NRIP1 Nuclear receptor SRE protein Number of related keywords found in the comprehensive annotation of the gene is displayed under each disease This number is hyperlinked to get detailed annotation of the gene Related keywords for the disease will be highlighted in the detailed annotation For example in the above figure 2 related keywords of breast cancer were found in Hs 111779 1 related keywords of bladder cancer were found in Hs 120759 To view genes involved in any one of the selected disease i Select the Diseases by clicking on the corresponding check boxes ii Select OR radio button at the bottom iii Click the Table View button List of genes involved in any one of the diseases will be displayed in the result window Il Genetypsc genomics simplified Biointerpreter User Manual To view t
30. Biointerpreter User Manual P BIOINTERPRETER New Biological Perspective to your Differentials Genetypsc genomics simplified 259 4th Cross Apurva Buildings 80 feet Road RMV 2nd Stage Bangalore 560094 India Telephone 91 80 40538300 200 Telefax 91 80 40538222 333 International Hotline 1 415 283 9698 Email contact genotypic co in Genetypsc genomics simplified Biointerpreter User Manual amp Getting Started About Biointerpreter Features Highlights Overview Biointerpreter Design and Contents User registration and Login e Login Registration Login page amp Searching amp Results Search options e Gene Identifier types e Paste IDs e Study name e P value cutoff e Search Examples What do get e Summary Report e Explain Categories Explanation of results Viewing the result categories amp interpretation of results Genetypsc genomics simplified Biointerpreter User Manual Getting Started About Biolnterpreter A web based efficient and easy to use interpretation tool that gives quick and complete interpretation of Microarray data by significantly reducing the analysis time from hours to minutes Features Highlights Helps derive full value of your Microarray study Automated biological analysis of Microarray data saves weeks without compromising on depth of information e Web based easy to use tool Specially designed f
31. Drug treatment 439 Number in the square bracket specifies number of genes in the genome differentially regulated for the corresponding drug response condition 29 Genetypsc genomics simplified Biointerpreter User Manual Hot Molecules Hot molecules have been categorized into i Multifunctional genes genes involved in more than 10 functions ii Involved in many diseases Genes involved in more than 8 diseases iii Expressed under various conditions Genes differentially regulated in more than 8 gene expression conditions iv Expressed in various cancer types Genes differentially regulated in more than 8 cancer types y Breast cancer marker No of category genes E Toxicity Marker 116 Breast cancer Marker 161 Expressed in various cancer types 780 E involved in Many Diseases 4106 e Sa under various conditions 2473 I functional genes 17053 Select All TableView Biointerpreter generates the hot molecule results in the above format Number in the Square bracket specifies number of genes in the database for the corresponding hot molecule category To view the gene list in the hot molecule category i Select the hot molecule category ii Click on the Table view button The list of genes associated with hot molecule category selected will be displayed at the result window with the following information e Query ID Unigene ID with link to detailed annotation Gene Nam
32. Modifications Protein Sorting Signal Peptide Proteolysis Signal Sequence Signal Recognition Protein Sorting Golgi Apparatus Receptors Receptor Ligand Ligand Mediation RNA Machinery Translation Transcription Splicing Rna Processing Rna Polymerase Rna Metabolism Rna Break Rna Binding Polyadenylation Cap Addition Signal Second Messenger Receptor Hormone Growth Factor Steroid Transduction Signalling Signaling Signal Transduction Cascade Signal Transduction Second Messengers Phosphatase Nuclear Kinase Cyclic Splice Variant Splicing Spliciozomes Spliciozome Splice Variant Stress Dna Repair Uv Stress Starvation Shock Irradiation Irradiate Hypoxia Dna Damage Suppressors Suppressor Suppress Suppressor Toxicity Toxicity Toxic Toxin Toxicology Poisoning Neurotoxin Neurotoxic Hepatotoxin Hepatotoxic Hemotoxin Hemotoxic Cytotoxicity Cytotoxic Transcription Transcription Transcription Transcription Regulation Transcription Factor Regulation Of Regulation Transcription Translation Translation Translated Transport Transportation Transport Pump Efflux Channel Transposable Transposons Transposon Transposable Element Jumping Gene Element Vasculogenesis Vasculogenesis Vascular Vesicle Vesicle Trafficking Vesicle Tethering Vesicle Priming Vesicle Trafficking Fusion Vesicle Docking Transcytosis 69 Genet
33. Select the cancer types v Select the desired regulation type Up Down Both from the pull down menu at the bottom vi Click the Pie Chart button Pancreas Blood Tumor 253 Tumof 36 1 Lymph Tumor 395 Bone Tumor 190 Kidney Tumor 30 Eye Tumor s4 Colon Tumor 1033 CancerName Count Blood Tumor 253 3 Bone Tumor 190 3 Colon Tumor 1033 S Eye Tumor 784 6 Kidney Tumor 30 1 Lymph Tumor 395 2 3 Pancreas Tumor 361 Number in the square bracket specifies number of genes in the genome differentially regulated for the corresponding cancer type 47 Genetypsc genomics simplified Biointerpreter User Manual Gene Ontology Gene Ontology Gene No of Ontology genes P value nucleus C 4119 cytoplasm C 1600 Ce f eo protein binding F 4136 EEE plasma membrane C ls821 9 mo cell cell adhesion P 47 O0 3 eae extraceluar regon O16671 o 1o collagen bindng D2 2 mo Select Al Clear And Or Default TableView Pie Chart Biointerpreter gives you list of significant Gene ontology with number of genes supporting the Gene ontology in the query list Number within the square bracket with Gene ontology specifies the number of genes supporting the Gene ontology in the genome To view the genes involved in the particular Gene ontology ii Select the Gene ontology by clicking on the corresponding check box iii Click the Table View button
34. acial phenotype 417 digestive alimentary phenotype 498 Number in the square bracket shows the number of genes supports the particular phenotype in genome 64 Genetypsc genomics simplified Biointerpreter User Manual Detailed Annotation This detailed annotation report displays a comprehensive annotation for the queried gene Unigene ID Retrieved from Unigene build 199 19 Jan 2007 Functional Annotation Lists the molecular and biological functions The functions were obtained from updated annotations available in our database Gene Expression Data Gene expression data is manually collected from published research articles These are usually differentials that are either validated or the top most up or down regulated genes from the study Genotypic technology unpublished data Genotypic Curation List of associated functions diseases for the gene with the number of pubmed references in bracket These phrases were obtained from published research articles by automated methods Genotypic Technology unpublished data Ex Apoptosis 5 This gene is related to apoptosis and there are 5 evidences references retrieved from Pubmed GenoRIF Genotypic References into Function Displays the references Evidence obtained from the published articles for the all functions diseases displayed in the Genotypic Curation These phrases were obtained from the published research articles by automated methods
35. all the selected pathways Refer the above fig Here is how a Select the Pathways by clicking on the corresponding check boxes b Select the AND radio button at the left bottom of the page c Select the Table view button The list of genes associated with pathway selected will be displayed below the pathway results with the following annotation Query ID Unigene ID with link to detailed annotation Gene Name Gene symbol Pathway ID KEGG ID with link to KEGG website Pathway name In the above figure the user has selected Regulation of actin cytoskeleton and cell communication We can get the genes which are involved in both the pathway by clicking on the table view Refer the table given below Query Unigene Gene id ID Symbol Gene Name PathwaylID PathwayName mellitus Antigen processing and presentation alpha Th F superfamily member 1 Transporter 2 ATF binding cassette sub family MDR TAP hsal4612 Antigen processing and presentation TAP Hs 502 TAP Unigene ID column is linked to detailed annotation for the gene Biointerpreter has comprehensive frequently updated annotation for the genes Pathway ID is linked to corresponding pathway in KEGG database If you click on hsa04612 it will go to corresponding pathway in the KEGG database 16 Genetypsc genomics simplified Biointerpreter User Manual Similarly we can get the genes which are associated with any one of the
36. ally P value less than 0 05 considered as significant Number of genes in a pathway in the query list is compared to the genes in the same pathway in the genome to generate the P Value 4 The entire contents in the current page can be exported to spread sheet Save the file in the local computer 5 User can view the genes associated with the pathway a Select the interested pathway Pathway No of genes P value Pathway 1E 09 1E 09 1E 09 1E 09 1E 09 1E 09 Regulation of actin cytoskeleton 218 E cell adhesion molecules CAMs 138 Cell Communication 117 E Type I diabetes mellitus 44 E Cell cycle 121 VEGF signaling pathway 76 Select pie chart to view the Graphical representation of the selected pathways Complement and coagulation cascades 69 la 1E 09 metabo 2 1E 09 Erd 4 Select table view to E One carbon Fotatel 1 1E 09 4 view the genes Natural killer cell mediated cytotoxci in the selected pathway fan Y 1E 09 Select All Clear And Or Defaultj Tableview Pie Chart Select AND to view the genes which are present in all the selected Pathways Select OR to view the genes present in any of the selected pathway a Select the check box es of interested pathway s b Select the Table view button at the right bottom 15 Genetypsc genomics simplified Biointerpreter User Manual Biointerpreter allows you to find genes which are associated with
37. check boxes ii Select OR radio button at the bottom iii Click the Table View button List of genes involved in any one of the function will be displayed at the result window 20 Genetypsc genomics simplified Biointerpreter User Manual To view the pie chart for the selected functions i Select the Functions ii Click the Pie chart button Angiogenesis 632 Fooptosis 2028 Antigen Processing And Presentation 1554 FunctionName Count Angiogenesis 682 4 Antigen Processing And Presentation 1554 7 Apoptosis 2028 Number in the square bracket shows the number of genes involved in the functions in the genome 21 Genetypsc genomics simplified Biointerpreter User Manual Gene Expression Expression Condition Immunomodulation 100 Cardio Vascular Disease 47 mmation eukemial1716 Stress 2843 el Infla 250 19 31 Biointerpreter generates the gene expression results in the above format i Expression condition Gene expression condition of the genes in various stages ii Up Number of up regulated genes in the query list in the corresponding gene expression condition iii Down Number of down regulated genes in the query list in the corresponding gene expression condition iv Both Number of genes which are up and down regulated in the corresponding gene expression condition v P value vi Number in the square bracket is th
38. e Gene symbol List of functions under Multifunctional gene List of Gene expression conditions under Expressed under various conditions List of cancer types under Expressed under various cancer types 30 Genetypsc genomics simplified Biointerpreter User Manual Unigene Gene g Gene Name apy es ID Symbol Cold sho domain Hs 69855 Hs 69855 T l containing EL Ovary RNA binding Skin T Cell division cycle 20 homolog 5 ireyisiae Ribosomal protein 516 Genetypsc genomics simplified Expressed in various cancer Expressed under Multi functional Various conditions genes types Bone Tumour Brain Tumour Cervix Tumour Colon Tumour i Eye Tumour Germ cell Tumour Liver Tumour Lung Tumour Lymph Tumour Muscle Tumour lacenta Tumour umour Testis Tumour Uterus Tumour Leukaemia Stress Normal Vs Cancer Cancer Stages Activation Cell Response to organic YO a m pi compounds Anti Cell Proliferation oxidant treatment Ae Atherosclerosis Cell yt en z B specific expression i Sa sation i con tcp ee Res onse response Growth factor Inf iat meam eee Metabolism Stimulated response Cell Cycle Stress Normal Vs Cancer Primary Tumor Vs Metastasis Viral Infection Cell specific expression 31 Biointerpreter User Manual Chromosome Chromosome No of lue genes g x al Chromosome 16 06 16 09 F 1E 09 58 1E 09 2 1E 09 1E 09 8 0 0001
39. e Swissprot ID Genetypsc genomics simplified Biointerpreter User Manual e TIGR ID e Searching the Human database with Mouse Agilent IDs Affymetrix IDs and Gene symbol e Searching the Human database with Rat Agilent Ids Affymetrix Ids and Gene symbol e Agilent Chip on Chip ID s You can choose the desired ID type from the drop down menu Paste IDs Copy your gene list and paste in the box provided For example we have provided some ids of different type to access those ids click Example IDs link Note The Ids should be separated by carriage return i e each ID should be in a separate line The gene identifier type should be unique i e All IDs should be of same ID type Study name Type the study name in the box provided Study name is for your reference it does not change the way program works Now click on the Submit button P value P value is the short term for Probability value It tells us about the probability of getting significant result from your list when compared to population Chi square test has been used to calculate the P value Chi square is a common statistical method used to compare the observed data and expected data Usually P value less than 0 05 considered as significant Genetypsc genomics simplified Biointerpreter User Manual Search Examples Example 1 BIOINTERPRETER New Biological Perspective to your Differentals Logout Instructions Purcha
40. e specified number of genes in the genome differentially regulated for the corresponding gene expression condition 22 Genetypsc genomics simplified Biointerpreter User Manual To view the genes which are differentially regulated for the particular gene expression condition Expression Condition P value fay Atherosclerosis 16 4 E cene Activation response 1285 ay Inflammation 250 ay Cell Cycle 277 fay Response to organic compunds 345 aq Myopathy 410 ay Anti oxidant treatment 447 ay Stress 2843 E Normal Vs Cancer 498 ay Cancer Stages 107 ay Primary Tumor Vs Metastasis 1847 E jother Diseases 74 ay Cancer specific 1734 E eene regulation 107 Select All Clear and or Default TableView Pie Chart Up 0 0001 Oo L i Select the gene expression condition ii Click on the Table View button List of genes which are differentially regulated in the selected gene expression conditions will be displayed in result window Each gene is supported by the type of regulation with number of sub conditions available for the particular gene expression condition Unigene Gene me Toxin nO Query id ciel Gene Name Immunomodulation Syndrome treatment Metabolism ID Cyclin Hs 19192 Hs 19192 CDK dependent None None None Up 1 kinase 2 Lipocalin 2 Hs 204238 Hs 204238 LCN oncogene Down 1 None None None 24p3 Leukemia inhibitory Hs 2250 Hs 2250 LIF
41. ease follow these steps 1 Make sure Allow Cookies is enabled in your browser 2 If you are using demo account make sure that you have not exceeded the maximum login limit which are 20 or 15 days from the first Activation Date 3 If you cannot remember the password please write to biointerpreter genotypic co in Genetypsc genomics simplified Biointerpreter User Manual Searching amp Results Once you reach the Biointerpreter Query page you can analyze your gene list with Biointerpreter Biointerpreter is an online tool with user friendly web interface It is biologists friendly too no special training such as advanced Excel needed to use the tool Savor TERPRETER Mew Biological Perspective to your Differentials Mouse Biointerpreter Brochure Welcome kavitha genotypic co in Full User Human Biointerpreter All fields are mandatory Select ID Unigene Id Hs 100915 Hs 100915 Paste ID s Hs 443430 Example le Hs 463421 n Hs 515005 Hs 632249 Study Name Exp1_uprequlated PValue Cutoff Stringent 0 01 Search options Gene Identifier types Biointerpreter allows you to query different types of gene Identifiers The gene identifiers could be any one of the following e Unigene e NCBI Gene ID e Gene Symbol e Genbank nucleotide accession e Genbank protein accession e Agilent ID e Affymetrix ID e Ensembl ID e PIR Accession e Nucleotide GI e Protein Gl e Swissprot accession
42. enase gamma butyrobetaine hydroxylase 1 Hs 386567 Hs 386567 GBP2 Guanylate binding protein 2 interferon inducible Hs 591996 Hs 591996 BBOX1 Hs 171695 Hs 171695 DUSP1 Dual specificity phosphatase 1 Hs 513617 Hs 513617 MMP2 Matrix metallopeptidase 2 gelatinase A 72kDa gelatinase 72kDa type IV collagenase Hs 351306 Hs 351306 SLC16A4 Solute carrier family 16 member 4 monocarboxylic acid transporter 5 Hs 380277 Hs 380277 DAPKI Death associated protein kinase 1 Hs 151254 Hs 151254 KLK Kallikrein related Ss 7 Hs 204238 Hs 204238 LCN2 11 Genetypsc genomics simplified Biointerpreter User Manual Result Categories The biological interpretations of the genes by Biolnterpreter were represented under multiple categories The categories are Function Disease Localization Protein Ligand Gene Ontology Pathway Mutation Hot molecules Chromosome Gene Expression Protein domain Tissue expression Drug response data Phenotype Function Significant molecular biochemical functions associated with the genes queried The list of functions was curated from annotation available in our database Disease Major disease associated with the genes queried Localization Major sub cellular localization of the genes in the query list These sub cellular localizations were curated from the updated annotation available in our database Protein Ligand A Ligand is a molecule which interacts with a protein by specifically bi
43. genesis Cell Functional Annotation Proliferation Gene Regulation Growth Factors And Regulators Immune Response Infection Neuronal Transcription Regulation 1 Transcription 4 Vasculogenesis 1 Cell Adhesion 4 AIDS 1 Apoptosis 1 Cell Division 3 Cell Migration 3 Cell Proliferation 5 Chromosomal Genotypic Curation Segregation 1 Cell Differentiation 4 Growth Factors And Regulators 5 Neuronal 2 Oncogenesis 1 Post Translational Modifications 1 Prostate Cancer 1 Protein Sorting 1 Receptors Ligand Mediation 2 RNA Machinery 4 Signal Transduction 1 Myopathy Cell specific expression Cancer specific Tissue Organ Specific Expression Viral Infection Cell Cycle The protein encoded by this gene is a member of the fibroblast growth factor FGF family FGF family members possess broad mitogenic and cell survival activities and are involved in a variety of biological processes including embryonic development cell growth morphogenesis tissue repair tumor growth and invasion This protein was isolated as a secreted factor that exhibits a growth stimulating effect on cultured glial cells In nervous system this protein is produced mainly by neurons and may be important for glial cell development Expression of the mouse homolog of this gene was found to be Gene Expression Data Gene Summary To view genes involved in any one of the selected functions i Select the Functions by clicking on the corresponding
44. gocyte Opsonization Natural Killer Cells Natural Killer Cell Lymphokine Innate Immunogen Immuno Immunized Immunize Immunity Immune Defense Cytolysis Chemokine Antigen Antibody Infection Pathogenesis Pathogen Invasion Infectious Infection Infected Infect Inflammation Macrophage Chemotaxis Neutrophil Cytokine Chemotaxin Chemotactic Wound Vaso Active Sertonin Redness Prostaglandin Prostacyclin Membrane Attack Lymphocyte Interleukin Interferon Inflammed Inflammatory Inflammation Ige Hypersensitivity Histamine Healing Fever Eosinophil C5A C3B C3A Bradykinin Membrane Syntaxin Synaptotagmin Synaptobrevin Membrane Fusion Fusion Metabolism Enzyme Metabolism Metabolic Enzymatic Catabolism Catabolic Anabolism Anabolic Negative Gene Negative Regulation Negative gene regulation Regulation 68 Genetypsc genomics simplified Biointerpreter User Manual Neuronal Spinal Neuronal Neuro Neural Nerve Brain Axon Oncogenesis Tumourogenesis Oncogene Oncogen Phagocytosis Phagocytosis Phagocytic Positive Gene Positive Regulation Positive Gene Regulation Regulation Post Signal Peptide Sulfation Seleno Prenylation Phosphorylation Translational Methylation Glycosylation Deamidation Clevage Carboxylation Modifications Acylation Acetylation Proteolytic cleavage Post Translational
45. he Table View button Query id ste ues Symbol Gene Name Bladder Blood Hs 108029 Hs 108029 SH3BGRL SH3 domain binding glutamic acid rich protein like Hs 109225 Hs 109225 VCAMi Vascular cell adhesion molecule 1 Hs 110364 Hs 110364 PPIC Peptidylprolyl isomerase C cyclophilin C Hs 111 7 9 Secreted protein acidic cysteine ror rich osteonectin Hs 11590 Hs 11590 Fascin homolog 1 actin bundling Hs 118400 Hs 118400 FSCN1 protein Strongylocentrotus purpuratus Apolipoprotein B including Ag x antigen Transcription factor 8 represses interleukin 2 expression 1946A 4 ATP binding cassette sub family G Hs 124649 Hs 124649 ABCG1 WHITE member 1 Number of related keywords found in the comprehensive annotation of the gene is displayed under each tissue This number is hyperlinked to get detailed annotation of the gene Related keywords for the tissue will be highlighted in the detailed annotation For example in the above figure 1 related keyword of Blood was found in Hs 108029 1 related keyword of Bladder was found in Hs 109225 43 Genetypsc genomics simplified Biointerpreter User Manual To view genes expressed in any one of the selected tissue i Select the tissue by clicking on the corresponding check boxes ii Select OR radio button at the bottom iii Click the Table View button List of genes expressed in any one of the tissue will be displayed in t
46. he Table View button The list of genes associated with the selected phenotype will be displayed at result window with the following information Query ID Unigene ID with link to detailed annotation Gene Name Gene symbol Phenotype ID Phenotype 61 B Genetypsc Biointerpreter User Manual Biointerpreter allows you to find genes which are associated with all the selected Mutations Here is how a Select the Phenotype by clicking on the corresponding check boxes b Select the AND radio button c Click the Table View button Phenotype Phenotype al adipose tissue phenotype 198 cardiovascular system phenotype 919 E feellular phenotype 630 craniofacial phenotype 417 ae E embryogenesis phenotype 803 endocrine exocrine gland phenotype 742 Efgrow th size phenotype 1527 Select All Clear And Or Default TableView Pie Chart In the above figure the user has selected cardiovascular system phenotype and craniofacial phenotype We can get the genes which have both the phenotypes by clicking on the table view Refer the table given below 62 Genetypsc genomics simplified Biointerpreter User Manual Gene list for Selected phenotype Description Click on Unigene to view detail annotation of the gene Unigene Gene phenotype Query id I nae Gene Name Id Phenotype D Hs 109225 Hs 109225 VCAM1 Vascular cell adhesion molecule 1 f system phenotype Hs 120759
47. he pie chart for the selected disease il Select the Diseases iii Click the Pie chart button Biointerpreter displays the pie chart in the result window Fmoebiosis 10 Bone Cancer 93 Breast Cancer 923 DiseaseName Amoebiosis 10 Bone Cancer 9 Breast Cancer 923 Number in the square bracket shows the number of genes involved in the disease in the genome 38 Genetypsc genomics simplified Biointerpreter User Manual Cellular Localization Cellular Localization a No of Localization genes P value E eytoplasmiseoay o eo E fovtoskaretonizs o j eo E Endoplasmic Reticulum 754 9 1609 E Eeracetuarinasa OO 2 j eos E ructeustaoss o a O eoo Plasma Membrane 2092 So oe i secrematiso7 27 16 09 Ei fiysosomestz2 gt oo E fcentrosomet120 2 oos m E E E C Integral to membrane 3451 selectall cear And Or Default _Tebieview Pie Chart Biointerpreter finds list of the significant sub cellular localization of the gene products in the query list i Sub cellular localization ii Number of gene s localized in the sub cellular location iii P value The number in the square bracket specifies the number of genes which belongs to the particular sub cellular location in the genome To view the genes localized in the sub cellular location i Select the Sub cellular Localization by clicking the corresponding check box ii Click the Table
48. he result window To view the pie chart for the selected Tissue i Select the tissue ii Click the Pie chart button Biointerpreter displays the pie chart in the result window Blood 14779 hfixed 32805 L Brain 31102 Lung 26230 Eye 22171 TissueName Blood 14779 Brain 31102 Eye 22171 Lung 26230 Mixed 32805 The number in the square bracket specifies the number of genes expressed in the tissue in genome 44 Genetypsc genomics simplified Biointerpreter User Manual Cancer Gene Expression Cancer Gene Expression Cancer Type P value Brain Tumores 22 ajil i Eye Tumore s a o Germcen Tumortoos 4 3 o adrenal Tumor 2o o 1 o Eo Bone Tumor 9q s a o 10s 3 Colon Tumortx033 16 2 a 1o penne ranra o f e To 16 09 Kidney Tumor 30 1E 09 Select All Clear And Or Default TableView Pie Chart BEE y c y c y E y y c y E y Biointerpreter generates the cancer gene expression output shown in the above format To view the genes differentially regulated in the cancer types i Select the cancer types ii Select AND radio button at the bottom iii Click the Table View button Cancer Type P value E prain Tumores fafa fa E Eye Tumort7z34 4 E cemce Tumors 2 0 E narena Tumoro f o 1 a fe a fo W Bone Tumor 190 1E 09 Select Al Clear And Or Default Fie Chart
49. interpreter displays the genes which are associated with any one of the selected protein domain on result window To view the Pie Chart for the selected pathways iv Select the protein domain v Click the Pie Chart button Biointerpreter displays the pie chart on result window Immunoglobulin 236 Homeodomain 192 ProteinDomainName Count Immuno globulin 256 2 Homeodomain 192 4 Number in the square bracket shows the number of genes have the particular protein domain genome 53 Genetypsc genomics simplified Biointerpreter User Manual Ligand Binding Protein Ligand Protein No of Ligand genes Tacrolimus 88 3 NAD 3941 16 09 NADH 145 31 08 NADPH 155 31 05 P value 1E 09 H 284 1E 09 Protein 435 Calcium 132 Select All Clear And Or Default Tableview Pie Chart Biointerpreter gives you list of significant protein ligands with number of genes supporting the protein ligand in the query list Number within the square bracket with protein ligand specifies the number of genes supporting the protein ligand in the genome 1E 09 1E 09 NADP 155 1E 09 To view the genes involved in the particular protein domain i Select the Ligands by clicking on the corresponding check box ii Click the Table View button The list of genes associated with the selected protein domain will be displayed at result window with the f
50. ive pulmonary disease COPD chronic bronchitis Obstructive emphysema Pulmonary Disease Cicatrix scar cicatrix cicatrice Coccidioidomycosis Coccidioidomycosis Valley fever Cockayne Weber Cockayne syndrome Neill Dingwall Syndrome Syndrome Colon Cancer Colorectal cancer bowel cancer adenomatous polyps colon cancer colorectal carcinoma colon carcinoma Color Blindness monochromasy color sensation color blindness Common Cold common cold Acute nasopharyngitis rhinovirus coronavirus echovirus paramyxovirus coxsackievirus Coronary Heart Coronary Artery disease arterial plaque atherosclerosis Disease Angina Arrhythmia Creutzfeldt Jakob Jakob Creutzfeldt Spastic pseudosclerosis abiotrophic Disease dementia corticopallidospinal degeneration corticostriatal spinal degeneration syndrome spongioform cerebral atrophy Crohn S Disease Crohn regional enteritis regional ileitis granulomatous enterocolitis segmental enteritis segmental ileitis terminal ileitis Lesniowsky Cryptococcosis Cryptococcosis European blastomycosis torulosis Cushing S hypercortisolism cushing Syndrome Cystic Fibrosis CFTR Cystic fibrosis Fibrocystic Disease Mucoviscidosis Dengue Fever Dengue Aedes aegypti break bone fever Flavivirus Diabetes Diabetes diabetic hyperglycemia IDDM NIDDM chamber pot dropsy thirst disease sugar disease sugar sickness GDM
51. l analysis Y Few days Significiont list of differentials FT Y Chromosomal significance T Disease significance Ontology significance Y Funticonal significance Localization significance Y Phenotype duos Ligand binding details Tissue expression Y Using Concer expression Y Few Woeks of Mediline and database searches Biointerpretor A Similar microarray data Brolein domains ae F iy A kN a i n i CIN d Y lt jusi Ew k Hot mollecules Biomarkers Protein interaction details 5 hours Y a Fi a A A ev N Biological interpretation of differentials Here we understand that the various open source and commercial tools available for biological data analysis provides answers to different pieces of puzzles but when all these pieces are combined to make a sense The result is again a puzzle or confusion The biggest part of the confusion is deriving biological significance using curated and comprehensive gene expression and literature data from other studies is still not available from any other source or tool Genetypsc genomics simplified Biointerpreter User Manual Biointerpreter Genotypic s Biointerpreter allows you to confidently analyze your microarray data without the issues that you face today e Provides 15 different biological views using
52. n the sub cellular localization in the genome 41 Genetypsc genomics simplified Biointerpreter User Manual Tissue Expression No of genes Tissue P value Bladder 8327 Blood 14779 leonessa e f eo leone marrowtoza o7 mo abrnenon mo mo Elcervntsaso f oo f EO T lcoiont 18606 s eo I Embryo 16524 120 1E 09 Select All Clear E And i Or Default Tableview Pie Chart Biointerpreter finds list of the significant tissues in which the query genes expressed in the above format i Tissue ii Number of gene s expressed in the tissue iii P value The number in the square bracket specifies the number of genes expressed in the tissue in the genome To view the genes expressed in the tissue location i Select the Tissue by clicking the corresponding check box il Click the Table View button No of Tissue genes P value ag 1E 09 Select All Clear And amp Or Default Tableview Pie Chart 42 Genetypsc genomics simplified Biointerpreter User Manual Biointerpreter will display the genes expressed in the particular tissue at result window with the following information Query ID Unigene ID with link to detailed annotation Gene Name Gene symbol All possible tissues To view genes localized in all the selected Tissue i Select the tissue by clicking on the corresponding check boxes ii Select AND radio button at the bottom iii Click t
53. nding to it A list of significant protein ligands found for the genes in the query list are presented in Biointerpreter Protein Ligand data were retrieved from KEGG Ligand database Gene Ontology Describes gene products in terms of their associated biological processes cellular components and molecular functions in a species independent manner Pathway Collection of manually drawn pathway maps representing molecular interactions and reaction networks for metabolism human diseases cellular processes etc These pathway details were obtained from KEGG PATHWAY Mutation A mutation is a change in the DNA sequence of a gene Mutations in the DNA sequence can alter the amino acid sequence of the protein encoded by the gene The 12 Genetypsc genomics simplified Biointerpreter User Manual table view describes list of significant genes corresponding to various kind of mutations in the query list Hot Molecules Hot molecules have been categorized into i Multifunctional ii Involved in many diseases iii Expressed under various conditions iV Expressed in various cancer types y Toxicity marker vi Breast cancer marker The table view describes the list of analogous genes to these hot molecules Chromosome A threadlike linear strand of DNA and associated proteins in the nucleus of eukaryotic cells that carries the genes and functions in the transmission of hereditary information The table view describes the list of chromosome
54. nes involved in the functions in the genome To view the genes involved in a function i Select the Function by clicking the corresponding check box il Click the Table View button The list of genes associated with function selected will be displayed at the result window with the following information Query ID Unigene ID with link to detailed annotation Gene Name Gene symbol Function 18 Genetypsc genomics simplified Biointerpreter User Manual To view genes involved in all the selected functions i Select the Functions by clicking on the corresponding check boxes ii Select AND radio button at the bottom iii Click the Table View button No of genes P value Function E lac tivation 4856 1E 09 nat a ee a age Processing ATA In the above figure the user would like to view the genes involved in both Angiogenesis and Antigen Processing amp Presentation Biointerpreter finds the genes involved in both of the functions and reports in the result window Gene list for Selected Significant Functions Description Click on Unigene to view detail annotation of the gene Antigen Unigene Gene er E r Processing Query id ID Symbol Gene Name Angiogenesis And E N Hs 109225 Hs 109225 VCAM1 Vascular cell adhesion molecule 1 E Hs 111779 Hs 111779 SPARC 2ecreted protein acidic Ie SA a rich osteonectin Hs 112408 Hs 112408 Si00A7 100 calcium binding Fascin homolog 1
55. ng Hs 2982780 Hs 298280 ATP5A1 mitochondrial Fi complex alpha subunit 1 cardiac muscle Link in the Unigene ID column will lead the detailed annotation for the gene Biointerpreter has comprehensive frequently updated annotation for the genes ProteinLigand ID is linked to corresponding protein ligand in KEGG ligand database 55 B Genetypsc Biointerpreter User Manual Similarly we can get the genes which are associated with any one of the selected protein ligands iv Select the protein ligand by clicking on the corresponding check box v Select the OR radio button at the bottom vi Click the Table View button Biointerpreter displays the genes which are associated with any one of the selected protein domain on result window To view the Pie Chart for the selected Ligand i Select the protein ligand ii Click the Pie Chart button Biointerpreter displays the pie chart on result window ProteinLigand NADPH 155 H 284 NADP 155 NADH 146 H20 787 NAD 194 ron 8 ProteinLigandName H20 787 NAD 194 NADH 146 H 284 Iron 78 NADPH 155 NADP 155 e u hy bo Ln de te te 5 Number in the square bracket shows the number of genes have the particular protein ligand binding sites in genome 56 Genetypsc genomics simplified Biointerpreter User Manual Mutation No of genes E Missense nonsense 1604 1E 09 lspci o o a Si Elkeguiator
56. ollowing information Query ID Unigene ID with link to detailed annotation Gene Name Gene symbol Protein ligand ID with link to KEGG ligand database Protein ligand Biointerpreter allows you to find genes which are associated with all the selected Protein ligands Here is how i Select the Protein Ligand by clicking on the corresponding check boxes ii Select the AND radio button iii Click the Table View button 54 Genetypsc genomics simplified Biointerpreter User Manual Protein Ligand Protein No of P value Ligand genes Tacrofmus t881 O norna f o o NaDH 146 a w9 naopen ass o o l ew e ER 7 1E 09 NADP 155 1E 09 W H 284 1E 09 Protein 435 1E 09 Select All Clear And Or Default TableView Pie Chart In the above figure the user has selected NAD and H We can get the genes which have both the protein ligand binding sites by clicking on the table view Refer the table given below Description Click on Unigene to view detail annotation of the gene Unigene Gene Query id ID aS Gene Name ProteinLigandID ProteinLigandName Hydroxysteroid 17 beta dehydrogenase 2 Ectonucleotide Hs 190977 Hs 190977 ENPP pyrophosphatase phosphodiesterase 2 autotaxin Hs 162795 Hs 162795 HSD17B2 Hs 202354 Hs 202354 DIO Deiodinase iodothyronine type II Hs 272813 Hs 2 2813 DUOXI1 Dual oxidase 1 ATP synthase H transporti
57. on Unigene to view detail annotation of the gene A Response Cancer Query id aeaii Aana Gene Name to Other drug mym Drugs treatment SH3 domain binding glutamic acid rich protein None Hs 108029Hs 108029 SH3BGRL Secreted protein acidic cysteine rich osteonectin Transcription factor 8 represses interleukin 2 expression CAP adenylate cyclase associated protein 2 yeast In the above figure for Hs 108029 under Response to Cancer drugs the result is Down 1 It specifies that Hs 108029 is down regulated in Response to Cancer drugs There is one sub condition under Response to Cancer drugs in which the gene is down regulated Note None indicates no data available for the gene under the drug response condition 2I Genetypsc genomics simplified Biointerpreter User Manual To view the sub conditions Click on the Down 1 You will get the following gene expression details at the bottom of the page Unigene ID Linked to Unigene PMID article s Pubmed ID from which the data has been curated PMID is linked to corresponding article in Pubmed Experiment Experiment details Condition Condition in which the genes are expressed Regulation Type of regulation UnigeneID _PMID Regulation Down Regulated Genes in Human Mammary Carcinoma cells MCF Letrozole 7aro Cells MCF 7 cells stably Anastrozole and Hs 108029 158316 4 Tamoxifen treatment response transfected with the aromatase
58. or the users who are most likely to be biologist Only tool providing curated gene expression data Flexibility to query with more than 12 gene identifier types Provides more than 15 biological views of the genes viz function pathway disease etc e Biologist friendly Advanced Excel and database skills not required Comes from India s first Microarray Company e Attention Microarray users with Biointerpreter you can now query with your Mouse IDs and compare to human data Overview Your microarray projects generate clusters of hundreds to thousands of differentially expressed genes Even with the help of comprehensive information resources and specialized skills you could spend weeks to derive biological significance from these gene clusters Finally in the interest of time the most interesting biological significances are picked up often missing the subtle and not so obvious ones You might worry that you may not have fully realized the value of your microarray data The Microarray workflow below shows how quickly Biointerpreter performs the biological interpretation of differentials as compared to any other tool that typically takes few days time to complete the analysis Genetypsc genomics simplified Biointerpreter User Manual Microarray Work Flow amp Biointerpreter l Project Planning sample preparation RNA Extraction GC Labelling Hybridization Feature Extraction Preliminary Statistical and Biologica
59. plication Recombination Polymerase Ligase Endonuclease Dna Machinery Dna Repair Dna Repair Mismatch Repair Excision Repair Drug Response Toxicity Toxic Pharmacokinetics P450 Drug Tolerance Drug Response Drug Resistance Drug Metabolism Drug Effect Drug Distribution Drug Absorption Dose Effect Bioequivalence Bioavailability Endocytosis Phagocytosis Pinocytosis Engulf Endocytosis Cell Eating Cell Drinking Exocytosis Vesicle Trafficking Vesicle Tethering Vesicle Priming Vesicle Fusion Vesicle Docking Exocytosis Extracellular Integrin Focal Adhesion Integrin Binding Focal Contacts Focal Matrix Adhesions Extracellular Matrix Remodeling Gene Regulation Transcriptional Regulation Temporal Regulation Repressible Repressed Regulation Regulates Modification Initiation Initiate Inducible Induced Gene Regulation Elongation Elongate Coordinate Allosteric Effects Growth Factors Ligand Hormone Growth Factor Thrombopoietin Neutrophin And Regulators Neurotrophins Myostatin Granulocyte Erythropoietin Colony Stimulating Hemostasis Styptic Hemostasis Hemostasia Haemostasis Haemostasia Coagulation Homeostasis Osmotic Osmosis Homeostatic Homeostasis Housekeeping Housekeep Cell Maintenance Immune Phagocytosis Macrophage Chemotaxis Neutrophil Dendritic Response Cytokine B Cell B Cell T Cell T Cell Pha
60. ritis reiter s disease Retinoblastoma ocular tumor of retina retinoblastoma Rheumatoid Rheumatoid arthritis rheumatic gout rheumatoid disease Still Arthritis Disease Juvenile Idiopathy Rhinitis Rhinits coryza rubor rhinitic Salivary Gland Salivary gland Cancer mucoepidermoid carcinoma Cancer Salmonella Salmonella typhoid paratyphoid Schizophrenia Schizophrenia dementia paranoid scleroderma scleroderma systemic sclerosis hard skin sclerodactyly Severe Acute Severe acute respiratory Syndrome atypical pneumonia SARS Respiratory coronavirus Syndrome Shigellosis Shigellosis bacillary dysentery Shigella Smallpox Small pox Variola Vaccinia Orthopoxvirus Spasm Spasm cramp muscle spasm Syndrome syndrome Tetanus Tetanus neurotoxin tetanospasmin Clostridium tetani lockjaw gt trismus Thalassemia Mediterranean anemia Mediterranean anaemia Cooley thalassemia thalassaemia Thrombosis Clotting coagulation clabber clot clog platelet thrombocyte thrombosis Thromboembolism coagulate Thyroid Cancer Thyroid Cancer papillary follicular papillary carcinoma follicular carcinoma Tinea Pedis Tinea pedis Ringworm Athlete s foot dermatophytosis palmaris Tuberculosis Pott s disease tuberculosis phthisis white plague king s evil lupus vulgaris Typhoid Fever Typhoid enteric Salmonella Typhi Ulcer ulcer lesion Viral Encephali
61. ry Guillain Barre Guillian Barre syndrome Landry s Ascending Paralysis Acute Syndrome Inflammatory Demyelinating Polyradiculoneuropathy acquired demyelinating neuropathy Head And Neck Head cancer Neck cancer squamous head and neck Cancer Heart Disease Heart disease cardiac arrhythmia cardiomyopathy Cardiomyopathy cardiomyopathic Hemophilia Hemophilia bleeder disease haemophilia uncontrolled bleeding Hepatitis Hepatitis Hepatocellular liver cancer hepatocellular carcinoma Carcinoma Herpes Simplex Herpes simplex Cold Sore Night Fever Fever Blister Herpes Zoster Herpes zoster shingles varicella zoster virus Histoplasmosis Histoplasma Histoplasmosis Human HPV skin warts Pappilloma virus Papillomavirus Hyperlipidemia hyperlipemia hyperlipaemia hyperlipidemia hyperlipidaemia hyperlipoidemia hyperlipoidaemia Infertility infertiliy sterility impotence impotency unfertile Influenza Influenza Flu Orthomyxoviridae Kidney Cancer Kidney cancer Renal cell carcinoma Lafora Disease Spinal bulbar muscular atrophy Lafora Baltic myoclonus Unverricht Leishmaniasis Leishmania sandfly kala azar black fever sandfly disease dum dum fever espundia Leprosy Hansen Mycobacterium leprae Lepromin test leprosy Leukemia leukemia leukaemia leucaemia cancer of the blood malignant neoplasm of blood blood cancer leukemic 72 Genetypsc
62. se Mouse Biointerpreter Brochure Welcome kavitha genotypic co in Full User All fields are mandatory Unigene Id Hs 100915 Hs 100915 Paste ID s Hs 443430 oe Hs 463421 5 a Hs 515005 Hs 6322495 Study Name Exp1_upregulated PValue Cutoff Stringent lt 0 01 Example 2 BIOINTERPRETER Mew Biological Perspective to your Differentials Logout Instructions Purchase Mouse Biointerpreter Brochure Welcome kavitha genotypic co in Full User All fields are mandatory Select ID Gene Symbol NAT ADH1B Paste ID s CEACAM3 ae CEACAM4 LIA CEACAMS Study Name Exp1_ downregulated PValue Cutoff stringent lt 0 01 Search Reset Cancel Genetypsc genomics simplified Biointerpreter User Manual What do I get Summary Window Back Comments Limit 300 Ids ID type Human SwissProt Study Name Up_regulated_set Export To Excel ID Pvalue Cutoff 0 05 Ids Entered 19 Non redundant Ids ois Number of Genes Found No of a Pathway Pathway W Cell cycle 121 Melanoma 75 Chronic myeloid leukemia 84 P value Glioma 70 Antigen processing and presentation 82 a m a E Hedgehog signaling pathway 59 a 8 Jak STAT signaling pathway 159 O a Ew ee ae TablevView Pie Chart eet Hematopoietic cell lineage 91 Jalal cytokine cytokine receptor interaction 261 Select All Clear Chromosome And Or
63. ses etc The link in the KEGG ID will lead the corresponding pathway in the KEGG pathway database Link to KEGG PATHWAY Similarity Description of the similarities sequence or structural of a protein with other proteins as derived from Swissprot 66 Genetypsc genomics simplified Biointerpreter User Manual List of functions curated and related keywords by Genotypic Function Related Keywords Activation Activator Activation Activate Ageing Senescence Aging Ageing Angiogenesis VEGF Endothelial Growth Endothelial Cell Growth Angiopoietin Angiogenetic Angiogenesis Angiogen Antigen Macrophage Dendritic B Cell B Cell Mhc Histocompatibility Processing And Antigen Presenting Cell Antigen Presentation Antigen Processing Presentation Apoptosis Suicide Programmed Cell Death Pro Apoptotic Pro Apoptosis Caspase Apoptotic Apoptosis Apoptogen Apoptin Anti Apoptotic Anti Apoptosis Autophagocytosis Type Il Cell Death Cytoplasmic Cell Death Autophagy Autophagocytosis Auto Phagocytosis Auto Phago Cytosis Biosynthesis Bio Synthetic Biosynthetic Bio Synthesis Biosynthesis Bio Synthetic Bio Synthesis Cell Adhesion Integrin Sticky Stick Selectin Catenin Cadherin Adhesion Adherence Adhere Cell Cycle Meiosis Mitotic Mitosis Mitogen Meiotic Cytokinesis Telophase S Phase Restriction Point Pro Phase Prophase Pro Metaphase
64. tis viral encephalitis Vitiligo vitiligo depigmentation hypopigmentation loss of melanin hypomelanosis leukotrichia Vonhippel Lindau Lindau angiomatosis Syndrome Yellow Fever yellow jack black vomit American Plague Aedes simpsoni Haemagogus Sabethes yellow fever 74 Genetypsc genomics simplified Biointerpreter User Manual List of Sub cellular localization curated by Genotypic with related keywords Sub cellular location Related keywords Centrosome centrosome central body Cytoplasm cytoplasm cytosol Cytoskeleton cytoskeleton Endoplasmic Reticulum reticulum Endosome endosome endocytic vesicles clathrin coated pits Extracellular extracellular serum Golgi Apparatus golgi vesicular tubular cluster Dictyosome Integral to membrane integral to membrane integral membrane Lysosomes lysosome Microsome microsome Mitochondria mitochondria Nucleolus nucleolus nucleole Nucleus nucleus nuclear transcription factor Peroxisome peroxisome selective protein import peroxin proteins Plasma Membrane plasma membrane plasmalemma cell membrane lipid bilayer Ribosomes ribosome polysomes Sarcoplasmic Reticulum Sarcoplasmic reticulum Secreted secrete exude exudate transude ooze Vacuoles vacuoles Vesicles vesicle vesicular cyst 75 Genetypsc genomics simplified
65. tudy name entered by the user in the previous page ID type The type of ID queried by the user IDs Entered Number of ids you have pasted in the Paste ids textbox Non redundant Ids If any id in the list is repeated the redundancy will be removed Only the unique list of ids will be taken to query the database e Number of genes found Number of genes found in the database for the IDs entered e Number of ids not found Ids not found in the database e The table views can be exported to Excel sheet and can be saved in the computer Back Comments Limit 300 Ids Study ID type Human Name Unigene Id Export To Excell New Search Ai Cutoff IDs entered ee nend a redundant No of IDs queried by ba Ids the user Number of a 204 204 fas not Found Found No of genes found in pan the database corresponding Pathway lt to gene identifiers queried No of Pathwav List of unique identifiers E Regetation of actin cytoskeleton 218 queried ey Cell adhesion molecules CAMs 138 A Cell Communication 117 e E type I diabetes mellitus 44 not found in the database E cell cycle 121 P va genes The user can view the list of genes found in the database by clicking Number of Genes Found button It displays the genes found with symbols and gene name Unigene in this page is linked to detailed annotation of the corresponding gene Hs 534699 Hs 534699 SCEL Sciellin Butyrobetaine gamma 2 oxoglutarate dioxyg
66. type on result window To view the Pie Chart for the selected Mutation e Select the Mutation type e Click the Pie Chart button Biointerpreter displays the pie chart on result window 59 Genetypsc genomics simplified Biointerpreter User Manual Regulatory 308 ssense nonsense 1604 Mutation Count Missense nonsense 1604 15 Regulatory 308 5 Number in the square bracket shows the number of genes supports the particular mutation type in genome 60 Genetypsc genomics simplified Biointerpreter User Manual Phenotype Phenotype No of Phenotype genes P value al adipose tissue phenotype 198 1E 09 cardiovascular system phenotype a cellular phenotype 630 1E 09 craniofacial phenotype 417 a 1E 09 al embryogenesis phenotype 803 1E 09 endocrine exocrine gland phenotype 1E 09 742 E grow th size phenotype 1527 1E 09 E hearing ear phenotype 257 1E 09 hematopoietic system phenotype 31 1E 09 928 F homeostasis metabolism phenotype 26 1E 09 1250 Select All Clear And Or Default TableView Pie Chart Biointerpreter gives you list of significant phenotype found in the query list Number within the square bracket with phenotype specifies the number of genes supporting the phenotype in the genome To view the genes for a particular Phenotype i Select the Phenotype by clicking on the corresponding check box ii Click t
67. y growing Data curated from over 500 000 Pubmed abstracts and topic specific Databases are used to index genes for disease function drug associations and other 15 classes The database is updated every month Genetypsc genomics simplified Biointerpreter User Manual User registration and Login Login Registration If you are a new user please register here Your Login details will be sent to you on the E mail provided during registration Login page Your email ID is the Login ID the password is case sensitive If the server is busy with other requests it will take up 10 seconds for logging into the program If the login fails check internet connection by visiting other sites If you can reach other websites try logging again If the login fails repeatedly try logging into the Mirror Server If you are using a Demo account verify if you have exceeded the number of logins or the demo period is completed You can always write to biointerpreter genotypic co in to obtain a new demo login or purchase a subscription Existing users login here New user Register here This is the Biointerpreter Login page Submit your login information and click Sign In J BIOINTERPRETER Mew Biological Perspective to your Differentials Home About Biointerpreter Instructions Purchase RegisterforDemo Brochure Sign in to Human Biointerpreter Version 1 1 Login Password Sign In Cancel If the login fails pl
68. ypsc genomics simplified Biointerpreter User Manual List of Diseases curated by Genotypic with related keywords Disease Name Addison s Disease African Trypanosomiasis Aids Alexander Disease Alopecia Alper S Syndrome Alzheimer Disease Amoebiosis Amyotrophic Lateral Sclerosis Anal Cancer Anemia Anthrax Arthritis Aspergillosis Asthma Batten Disease Bladder Cancer Blastomycosis Bone Cancer Brain Tumor Breast Cancer Canavan Disease Related keywords Addison adrenal insufficiency hypocortisolism Adrenocortical hypofunction cortical insufficiency adrenocortical insufficiency bronzed disease bronze skin disease chronic hypoadrenocorticism melasma suprarenale suprarenal melasma Sleeping sickness trypanosomiasis tsetse fly Trypanosoma brucei hiv aids human immunodeficiency Kaposi sarcoma acquired immunodeficiency Alexander disease Leukodystrophy Megalobare Panneuropathy Hyaline Inclusion Megalencephaly alopecia Alper s disease progressive infantile poliodystrophy Alzheimer Presenile dementia senile dementia Primary Senile Degenerative Dementia Amoebiasis Entamoeba histolytica Amoeba ALS Amyotrophic Lateral sclerosis Lou Gehrig s disease Maladie de Charcot Anal Cancer colorectal cancer human papillomavirus HPV anaemia anaemic anemic Anthrax Bacillus anthracis splenic fever Woolsorters disease Ragpickers disease
69. ytso 6 mo Eifsmat insertionstess o mo Mutation P value Ecompiex rearrangementsi20ay 4 1o leros insertions 3 vooor Elsman naesta SiS leros aeresonsts Select All Clear And Or Default TableView Pie Chart Biointerpreter gives you list of significant mutation in the query list Number within the Square bracket with mutation specifies the number of genes supporting the mutation type in the genome To view the genes for a particular mutation type i Select the Mutation by clicking on the corresponding check box ii Click the Table View button The list of genes associated with the selected mutation will be displayed at result window with the following information Query ID Unigene ID with link to detailed annotation Gene Name Gene symbol Mutation type with Link to Human Gene Mutation Database 57 Genetypsc genomics simplified Biointerpreter User Manual Biointerpreter allows you to find genes which are associated with all the selected Mutations Here is how a Select the Mutation by clicking on the corresponding check boxes b Select the AND radio button c Click the Table View button Mutation No of genes P value Mutation TlMsserse nonsense i604 E Splicing 776 1E 09 1E 09 1E 09 Small insertions 656 1E 09 es ae 16 06 Regulatory 308 Gross insertions 182 3 0 0001 1 al Small deletions 927 al Small indels 34

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