PosMed (Positional Medline) User Manual
Contents
1. any ui 40 C check all 30 set as target z 20 B with keyword Find TE E Bi without keyword m m Adipog A unknown 1999 2000 2001 2002 2003 2004 2005 2006 2007 2008 inc Adipor2 publication year 7 4 S noninsulin dependent dia show digest order by fact 7 Ai v ADIPOR1 1 20 of 128 1 next O I Sv adiport 1 7 Pattern of expression of adiponectin receptors in human adipose tissue depots E WS Deitagen and Lexicon Knoc and its relation to the metabolic state PMID 17607322 im Edn1 International journal of obesity 2005 2007 Dec 7 ip Amh OBJECTIVE To investigate whether adiponectin receptor genes AdipoR 1 and AdipoR2 mi expression in human subcutaneous SAT and visceral VAT adipose tissue in severely obese patients with or without diabetes is related to adiponectin gene APM1 expression and in vivo 7 dm Agrp metabolic parameters Meis onc cdd odios Top fifty related molecules and any M lt taunted diseases are displayed as biological Mouse Locus C check all oer et as target objects initially You can select a Arabidopsis Locus Find TN EE We Acetyl CoA particular condition from the pull esaad Hependent dia E Ve Hypoxantnine down menu e g Metabolite F In Ppara j 7 e L Noradrenaline I Sv ADIPOR1 7 V Oleic acid 7 iu Sv Adiport 7 S Adenosyl L methionine put mnc en cwewedcc Click the Find image to display the Metabolite v Giycorcl k2. 119383102 2 Gene expression of adiponectin receptors in human visceral and subcutaneous adipose tissue is related to insulin resistance and metabolic parameters and is altered in response to physical training PMID 17878241 Diabetes care 2007 Dec OBJECTIVE Adiponectin receptors 1 and 2 AdipoR 1 and AdipoR2 respectively mediate the effects of adiponectin on glucose and lipid metabolism in vivo im Adipor1 adiponectin receptor 1 references MGI 1919924 CAGE Mm 1 136231891 136248748 ii Adipog adiponectin C1Q and collagen domain containing references MGI 106675 CAGE 4m 16 23061870 23073302 dm Adipor2 adiponectin receptor 2 references MGI 93830 CAGE Mm 6 119318769 119383102 18 January 5th 2009 Copyright O 2005 2009 RIKEN 5 3 Relationship to gene cluster associated with the gene When you click 3 gene Adipogq a list of relationships to genes associated with the gene 1s displayed Search gene keyword diabetes OR insulin Threshold P 0 01 Mouse Locus i show qraph Symbol Adipor1 Name adiponectin receptor 1 ID MGI 1919924 set as target m 136 P value B 185 Link to MGI CAGE 0 Position Mm 1 136231891 136248748 P value 1 68E 388 Co citation P value 1 68E 388 Mouse Locus Co citation mm show araoh ee Symbol Gpr39 Rif Name G protein coupled receptor 39 P value ID MGI 1918361 set as target P value 7 00E 3 Link to MGI
3. CAGE Position Mm 1 127504539 127701399 January 5th 2009 19 Mouse Locus keyword r E show graph Symbol Adipoq t Name adiponectin C1Q and collagen domain P value 7 90E 2915 Keyword diabetes OR insulin containing Other aliases adipoQ adiponectin GBP28 apM1 adipo Acrp30 Acdc ID MGI 106675 B 2927 Link to MGI CAGE Position Mm 16 23061870 23073302 Copyright 2005 2009 RIKEN 5 4 Relationship between the gene and the keywords When you click 4 the keyword icon document digests describing both the keywords and the gene Adipoq adiponectin etc are displayed In the document digest display the gene name and the keywords are highlighted with light green adiponectin and red diabetes or insulin respectively In the default display sequence documents including the keyword s are ranked higher Click a document number in order to transfer to PubMed at NCBI All Hits Adipoq te show graph Symbol Adipoq Name adiponectin C1Q and collagen domain containing Other aliases adipoQ adiponectin GAP28 apM1 adipo Acrp30 Acdc ID MGI 106675 B373 bw 3038 in ADIPOQ adiponectin C10 and collagen domain containing HGMC 13633 CAGE Hs 3 188043156 188058945 23073302 in Adipoq adiponectin C1Q and collagen domain containing RGD Rn 11 78908280 799821104 Reported Adipoq is associated with the keyword as follows all 3038 2773 mouse mutant HsPPI 0 2 M
4. Position Mm 6 119318769 119383102 Human Locus IN NN show araoh Symbol ADIPOR1 Name adiponectin receptor 1 Other aliases ACDCR1 CGI 45 CGI45 FLJ25385 FLJ42464 icem PAQR1 TESBP1A ID HGNC 24040 3 Link to HGNC CAGE Position Hs 1 201176575 201194033 Co citation Disease lt gt P value Bi T show qraph 0 i Name non insulin dependent diabetes mellitus P value 1 17E 10 ID RIO CRIO010018001797 25 37365 a 12 January 5th 2009 keyword T P value 2 49E 4632 Keyword diabetes OR insulin lt gt keyword T P value 2 63E 121 Keyword diabetes OR insulin keyword T P value 2 87E 84 Keyword diabetes OR insulin lt gt keyword T P value 3 94E 17 Keyword diabetes OR insulin keyword P value 0 Keyword diabetes OR insulin gt Copyright 2005 2009 RIKEN 5 2 Relationship between the gene and another gene When you click 2 the relationship document digests that include both the genes are displayed In the document digest display the gene names and the keywords are highlighted with light blue Adiporl etc light green Adipoq etc and red diabetes or insulin respectively Additional biological objects are displayed in gray In the default display sequence the documents including the keyword s are ranked higher Click a document number in order to transfer to PubMed at NCBI The hit list box The hit and related molecules tabs p
5. gene name search clear ecent 4 years 4 show 20 Tutorial English Japanese Sample trial search diabetes related genes on chr 1 in mouse PosMed Positional MEDLINE assists your positional cloning studies Since whole genome sequences were first elucidated Knowledge based ranking of candidate genes has become one of the most important bioinformatics tasks in the forward genetics and positional cloning approaches to identify phenotype responsible gene mutations This task requires creating a farm of artificial intelligence that can solve a genetic researcher s problems by learning computationally a vast amount of information accumulated in documents and published data Pos n mu Phenotypic Keyword a We have developed a system named PosMed an artificial intelligence that guides you to the key information waiting to be discovered in the sea of data January 5th 2009 Copyright O 2005 2009 RIKEN The search result page of PosMed search gene Select Interval with OmicBrowse chromosome 1 v position from 90M keyword diabetes OR insulin download annotation download rank list set as target add comment E check all 1 o p Ngapa pHNpN E Im insig2 7 mino E Serpinb2 7 ip Adora1 im Ptprc 7 im Adiport E im Cxcr4 dm Mapkapk2 ag Capn10 E im Bel2 E a Ramp1 7 4m Pigr O Am Lct 7 Am Dbi E Im Pdcd1 7 4m i119 7 im Myog ip Gpc1 E d
6. l All Hits ii Adipor1 download rank list E check all 1 N N Ao a b MA b MA ho o e gt 5 o oo NoMe WR SB SD January 5th 2009 eo p Nn mp mh p yw ra Im Insig2 fio E agp Serpinb2 F dm Adora1 Im Ptprc E Im gt gt Adipor1 ig Cxcr4 ag Mapkapk2 E Capn10 O hm Bci2 aig Ramp1 E im Pior 7 dm Let 7 4m Dbi 7 Ag Pdcd1 7 ding 7 Am Myog E ig Gpc1 dm Tnnt2 F da Ctse a Sox13 ir Related molecules and lt gt ig Adipog Ei NES Relation Emi show graph lt gt P value 1 82E 499 B153 5E 120 mouse mutant 0 HsPPI 0 MEDLINE 153 mouse gene record 0 Link to MGI CAGE REACTOME 0 Position Mm 16 23061870 23073302 show graph Symbol Adipoq Name adiponectin C1Q and collagen domain containing Other aliases adipoQ adiponectin GBP28 apM1 adipo Acrp30 Acdc ID MGI 106675 Symbol Adipor1 Name adiponectin receptor 1 ID MGI 1919924 Link to MGI CAGE Position Mm 1 136231891 136248748 all 120 153 mouse mutant HsPPI 0 0 MEDLINE mouse gene REACTOME 0 0 120 153 record 0 0 Adipor1 related entities keyword diabetes OR insulin year all P ind any 50 Bo i check all E Jb set as target download draw Z 20 e B with keyword Find E Ag i E E W without keyword ui iw Adipoq s unknown 1999 2000 2001 2002 2003 2004 2005 2006 2007 2008 R Adipor2 pub
7. physical terms e g binds and highlight these terms n 2 n j v v Pri keyword diabetes OR insulin a Ce diabetes OR insulin 40 regulatory gt al 20 m Bi with keyword 10 4 B without keyword unknown 1999 2000 2001 2002 2003 2004 2005 2006 2007 2008 publication year documents o show digest v order by fact Y 1 20 of 128 1 next 1 x Adiponectin and its role in cardiovascular diseases PMID 18336252 Cardiovascular amp hematological disorders drug targets 2008 Mar Adiponectin binds two receptors AdipoR 1 and AdipoR2 year all The published year of documents is narrowed down by the year all lusum pull down menu You can select years from 1999 to the current year 2000 or any with unknown published years The default setting is all 2001 17 January 5th 2009 Copyright O 2005 2009 RIKEN show digest The show pull down menu has two modes the default is the digest all mode to display the minimum sentences including keyword s and title biological objects and the other one 1s the all mode to display whole text order by fact The order by pull down menu enables us to change the display relevance sequence of the hit documents by biological objects keyword s or recency their recentness The default 1s the fact mode to display sentences including previously selected biological objects in this case AdipoR1 Adiporl and the biological object AdipoR2 Ad
8. 748 Linkto MGI CAGE 4T 3244 docs P value 1 82E 499 im Adipoq 13773docs Position Mm 16 23061870 23073302 Linkto MGI CAGE 4 sx 4378hits P value 2 49E 4632 diabetes OR insulin Tree display mode shows a compact list of the search results in a hierarchical structure with minimum information similar to the Simple mode 6 Adiporl adiponectin receptor 1 im Adipor1 172 docs Pvalue 1 82E 499 Position Mm 1 136231891 136249748 Linkto MGI CAGE L244 docs Pvalue 1 82E 499 L im Adipoq 3773 docs Position Mm 16 23061870 23073302 Linkto MGI CAGE Lx 4378hits P value 2 49E 4632 L diabetes OR insulin Graph display mode shows a list of the search result with more information Each result indicates the search path from keyword right to gene left 6 Adipor1 adiponectin receptor 1 Interval Mouse Locus Co citation Mouse Locus Keyword S lt gt i show qraph Rif M show graph t Symbol Adipor1 P value 1 82E 499 Symbol Adipoq P value 2 49E 4632 Name adiponectin receptor 1 B 244 Name adiponectin C1Q and collagen Pd P value 1 82E 499 domain containing om sl ID MGI 1919924 set as target Other aliases adipoQ adiponectin 172 GBP28 apM1 adipo Acrp30 Acdc Link to MGI CAGE ID MGI 106675 Position Mm 1 136231891 136248748 B 3773 Link to MGI CAGE Position Mm 16 23061870 23073302 January 5th 2009 Copyright O 2005 2009 RIKEN 4 Understand th
9. EDLINE mouse gene REACTOME 3 4 2035 37685 record 0 1 Adipoq related entities keyword diabetes OR insulin year all Find a 1000 ES zo E check all u amp 00 Ex Eq set as target download 400 E with keyword draw 200 HEN Find unknown 1999 2000 2001 2002 2003 2004 2005 2006 2007 2008 E im Lep publication year 7 ii Pzp 4 20 of 300 1 next 7 m a E im Cyp2e1 1 Adiponectin and risk of coronary heart disease in older men and women PMID 18583765 E im Crd The Journal of clinical endocrinology and metabolism 2008 Sep C a Vamp2 RESULTS Adiponectin exhibited significant negative correlations with baseline adiposity 7 ap Gpr120 insulin resistance dyslipidemia inflammatory markers and leptin 7 ag insig i 7 im Tir P Rou gnon Heberden disease references He Cholesterol references KID COQDO03648 E Csf3 2i Adipog adiponectin C10 and collagen domain containing references MGlI 106675 CAGE a csi Mm 16 23061870 23073302 im Cst3 cystatin C references MGL102519 CAGE Mnv2 148563189 148566926 7 aig Cxch 1 ep leptin references MGE 104663 CAGE Mm 8 289010231 23023886 Additional biological objects are highlighted in gray e g leptin Other related molecules are listed 1n the left yellow box Click the images to display the relationships and to find further related biological objects 20 January 5th 2009 Copyright O 2005 2009 RIKEN
10. PosMed Positional Medline User Manual RIKEN Bioinformatics And Systems Engineering BASE division Division Director Tetsuro Toyoda Index LL Sooo sila ks a S e oerte OMM A A INDIEN EUM M DE 2 2 De hesearci COH D BUTS aeiiaaie iiki iaaii 4 o Spe ity the display conditions noce op IERI E DINE E FUE PUR d Et ad anias aiai 6 4 Understand the relationship between the candidate genes and the keyword 10 4 1 Relationship displayed in the Simple mode eH 10 4 2 Relationship displayed in the Tree mode eeeeeeee 11 4 3 Relationship displayed in the Graph mode eee 11 5 Browsing the details of eter cc ccs cence ee anatase oeecess 12 5 1 Relationships between the gene and the keywords eee 12 5 2 Relationship between the gene and the Gene cece ccc cecceeccecceceeeseeceeceeseececens 13 5 3 Relationship to gene cluster associated with the gene ccccccccecceeceeceeseeseeeees 19 5 4 Relationship between the gene and the keywords eee 20 The URL of this website is http omicspace riken jp If you have any questions and comments please feel free to send to omicspace gmail com January 5th 2009 Copyright O 2005 2009 RIKEN 1 Introduction PosMed is RIKEN BASE s original system which possesses inference type full text search functions At first PosMed performs a full text search of the docu
11. PosMed system 5 1 Chromosome pull down menu and base pair entry boxes 2 Genomic band entry box 3 Accessions entry box At the stage of 2 when the menu condition is selected as genomic interval or multiple intervals this part is displayed as 1 to specify genomic interval s In the case of genomic interval band or multiple intervals band this part is displayed as 2 to enter band name eg 20p13 In the case of accession or multiple accessions this part is displayed as 3 to enter accessions And also in the case of genomic interval and accessions both 1 and 2 are displayed at the January 5th 2009 Copyright O 2005 2009 RIKEN same time 6 Clear button to reset chromosome pull down menu and erase the base pair entry boxes 7 Pull down menu specifying a genome version For this manual the genome version we use is NCBIm36 8 Keyword entry box PosMed enables us to specify more complex conditional equations using OR caps AND caps parentheses double quotation marks for phrases wild card asterisk and question mark NOT caps and WHERE caps Keyword format in the Genome Browser amp PosMed system Phrase specification group with e g retinitis pigmentosa Treatment of space as AND operator asterisk Wild card e g diabet matches diabetes diabetic etc question mark e g ppar matc
12. abetes OR insulin CAGE v0 c om The maximum number of hit entries is 300 in the hit list box January 5th 2009 Copyright O 2005 2009 RIKEN 2 Specify the search conditions The search condition section has some pull down menus and entry boxes as below 2 3 5 6 search gene condition genomic interval species Mouse g Pos 4 chromosome 1 position from 71607120 to 101445287 version NCBIm36 lt 7 keyword diabetes OR insulin gene name recent 4 years 4 show 20 8 9 10 11 12 18 14 1 Search target pull down menu The menu items are any gene metabolite drug cell mutant disease document set dictionary and database According to the search target each search tool shown previously will be displayed 2 Search condition pull down menu 23 66 Available conditions are gene name genomic interval multiple intervals genomic interval band multiple intervals band accessions e g MGI 107357 HGNC 6079 multiple accessions and genomic interval and accessions 3 Species pull down menu The menus are any mouse and human For this manual the species we use is M musculus 4 Select Interval with OmicBrowse button At the stage of 2 when the menu condition is selected as genomic interval or multiple intervals this button is displayed with 5 Click this to display OmicBrowse in the
13. cuments Number of documents describing Number of documents describing the gene both genes describing the gene ll January 5th 2009 Copyright O 2005 2009 RIKEN 5 Browsing the details of hit results 6 Adipor1 adiponectin receptor 1 Interval 3 lt Locus show graph show graph domain containing Other aliases adipoQ adiponectin GBP28 apM1 adipo Acrp30 Acdc ID MGI 106675 E3773 Link to MG Position M CAGE 16 23061870 23073302 1 2 5 1 Relationships between the gene and the keywords 4 When you click 1 the gene various inference relationships from the gene to the corresponding biological objects are displayed Search gene keyword diabetes ORinsulin Threshold P 0 01 Mouse Locus Co citation Mouse Locus P valie 1 82E 499 i show qraph i show graph Symbol Adiport Bye Symbol Adipoq Name adiponectin receptor 1 ID MGI 1919924 set as target Name adiponectin C1Q and collagen domain containing P value 1 82E 499 Other aliases adipoQ adiponectin GBP28 apM1 adipo 1472 nf e Acrp30 Acdc Link to MGI CAGE ID MGI 106675 Position 14m 1 136231891 136248748 3773 Link to MGI CAGE Position 14m 16 23061870 23073302 P value s 0 Co citation Mouse Locus EN c E show araoh mye Symbol Adipor2 Name adiponectin receptor 2 P value P value 2 18E 1162 Other aliases D6Ucla1e 0 B 294 ID MGI 93830 148 Link to MGI CAGE
14. e relationship between the candidate genes and the keyword 4 1 Relationship displayed in the Simple mode Rank order Gene symbol and name 6 Adiporl adiponectin receptor 1 5 gt im Adipori E472 docs Pvalue 182E 499 Position Mm 1 136231891 136248748 Linkto MGI CAGE 4 So44docs Pvalue 182E 499 3 im Adipoq 237723 docs Position Mm 16 23061870 23073302 Linkto MGI CAGE 2 x 4378hits p value 2 49E 4632 1 p diabetes OR insulin The order from 1 to 5 indicates the search path from keywords bottom to genes top 1 A keyword icon indicates the keyword s entered in the keyword entry box previously 2 An arrow icon indicates the relationship between the keyword s and a gene with a p value T x 4378 hits P value 2 49E 4632 Number of document describing both the keywords and the gene 3 A Mouse gene icon indicates an intermediate path has relationships with both the keyword s and gene im Adipoq Bar docs Position Mm 16 23061870 23073302 Linkto MGI CAGE Number of document describing the gene 4 An arrow icon indicates relationships between two mouse genes 4 244 docs Pvalue 1 82E 499 Number of documents describing both the genes 5 A Mouse gene icon indicates a gene within the interval im Adiport 5 1472 docs P value 1 82E 499 Position IMm 1 136231891 136248748 Link to MGI Gene symbol Synthesis P val
15. eyword search box Click the go button to find a biological object of Cetyl CoA interest in this box e g Glycerol 16 January 5th 2009 Copyright O 2005 2009 RIKEN 5 2 4 Documents section The documents section has three convenient functions to find desired documents The functions are the show pull down menu order by pull down menu year pull down menu and Find keyword diabetes OR insulin year all E 30 20 E B with keyword Zar The charts indicate the B without keyword unknown 1999 2000 2001 2002 2003 2004 2005 2006 2007 2008 number of documents publication year show digest order by fact 4 20 of 128 1 next 1 Pattern of expression of adiponectin receptors in human adipose tissue depots and its relation to the metabolic state PMID 17607322 International journal of obesity 2005 2007 Dec OBJECTIVE To investigate whether adiponectin receptor genes AdipoR 1 and AdipoR2 expression in human subcutaneous SAT and visceral VAT adipose tissue in severely obese patients with or without diabetes is related to adiponectin gene P1 1 expression and in vivo metabolic parameters The keyword pull down menu enables us to change the display sequence of the hit documents by keyword s or biological terms The default is the previously entered keyword s in this case diabetes OR insulin Select physical to superordinate documents including
16. hes ppara ppare ppard etc Boolean operator NOT caps e g diabetes NOT type 1 Subquery WHERE caps e g plant WHERE synapse Note PosMed searches mouse genes by plant and synapse The search result of plant 1s displayed preferentially 9 Gene name entry box to specify as determinate targets e g Irs1 insulin receptor substrate 1 10 Execute button to search 11 Clear button to erase the keyword entry box and the gene name entry box January 5th 2009 Copyright O 2005 2009 RIKEN 12 Execute button to search with the specified number of years The default number is set to 4 This button is linked with the recent years pull down menu as below 13 Recent years pull down menu Available years are from 2 to 9 14 Show pull down menu Available numbers are 5 10 20 50 100 200 and 500 3 Specify the display conditions 1 2 3 All Hits check all 5 i Total Hits 50 4 805 sec Simple Mode v mouse mutant human gene record MEDLINE sentence mouse gene record W im irs1 OMIM PPI REACTOME rat gene record dm Capn10 Associate the keyword with entities co cited within the same sentences v dm Inpp5d Further associate the entities with entities co cited within the same sentences v V m Psmdt e E a E ouam 1 next display mode Simple v 7 l 8 9 1 Open all hits button Click this button to show or close a list of genes If you check some of the h
17. iO pmd cokagen d oman conbuing adpon adponen GHP acit adeo Ang Arde Adipert A E keyword Sahiti OR inguin pear M ay LT ine a 5 LLE fiaa i F tid 2 1 E g Eee Ul v Adigoq i PHA Gi ia DM IMM GM E lin vr sape Cl ne SF insn ingelin dependant dia show Get arger ty BE downisad E im arom 1209163 Page 1 ras e sape 1 v AdipoR 1 mediates the anorexgenic and insulintieptin loe actions of adiponectin F1 SS pugn ant Lexicon Knee iri thee Fypeothalamis SD pup 13394428 D NE FEES infers 2008 Apr 30 E i imh AdipoR 1 mediates the anorexigenic and iriullini Me actions of adiponectin ia the ypothalamus EZ ane Copyright O 2005 2009 RIKEN 5 2 2 Hit document tabs These tabs indicate the number of hit documents in each document set In the case of mouse the the information MEDLINE gene description of MGI PPI description of the HPRD and REACTOME description of BioPAX The number of hit documents which contain the document sets for inference search process are mutant keywords are highlighted in red The default setting is all REACTOME 0 0 MEDLINE 3035 3768 mouse gene record 0 1 mouse mutant 344 HsPPI 0 2 all 3038 3773 Click a tab to display the corresponding document digests as described above e g The transition from all to mouse mutant MEDLINE 3035 3766 mouse gene REACTOME other record 0 1 0 0 databases o Adi
18. ipor2 Select relevance to superordinate documents including keywords diabetes or insulin and highlight these terms The recency mode superordinates the latest sentences You can download the list of all documents by clicking the download button The list has information about the PMID PubMed identifier title name of the journal published year and date abstract and links to NCBI Click the Find image to display the keyword search box Click the go button to superordinate documents including the highlighted keyword of interest e g lipid Keyword keyword Physical year all v Find 40 30 lipid E TH ym 10 4 id Bi without keyword 3 Ii close unknown 1999 2000 2001 2002 2003 2004 2005 2006 2007 2008 publication year show digest v order by fact M 1 20 of 128 1 next 1 x Tissue specific effect of dietary cysteamine on expression of adiponectin receptors in rats PMID 17696487 Journal of agricultural and food chemistry 2007 Sep 19 Adiponectin is synthesized by adipocytes and affects glucose and lipid metabolism by binding to its receptors AdipoR 1 and AdipoR2 im Adipor1 adiponectin receptor 1 references MGI 1919924 CAGE Mm 1 136231891 136248748 ii Adipog adiponectin C1Q and collagen domain containing references MGI 106675 CAGE Mm 16 23061870 23073302 im Adipor2 adiponectin receptor 2 references MGI 93830 CAGE Mm 6 119318769
19. its you can set them as the next search targets by clicking set as target and download them as an excel file by clicking download All Hits V check all setas target Total Hits 50 4 805 sec Simple Mode V mouse mutant V human gene record V MEDLINE sentence V mouse gene record V E irs1 V OMIM V PPI V REACTOME V rat gene record 2 v Capn10 Associate the keyword with entities co cited within the same sentences v 3 v dm Inpp5d Further associate the entities with entities co cited within the same sentences v 4 v ig Psmd1 R en LZ ewaal4 1 next display mode Simple 6 All Hits Total Hits 50 4 805 sec Simple Mode V mouse mutant V human gene record V MEDLINE sentence V mouse gene record V OMIM V PPI V REACTOME V rat gene record Associate the keyword with entities co cited within the same sentences v Further associate the entities with entities co cited within the same sentences v 1 next display mode Simple v January 5th 2009 Copyright O 2005 2009 RIKEN 2 Number of hits and time taken for the search 3 Search path display mode pull down menu and path list Simple Mode Users can check document sets for inference search process Expert Mode The display condition part expands with all search path with neural weight pull down menu Users can check path and select neural weight for inferential search proces
20. lication year r iE rm non insulin dependentdia chow digest order by fact 7 in Sv ADIPOR1 1 20 of 153 1 next E Ii Sv adiport 1 AdipoR1 mediates the anorexigenic and insulin leptin like actions of adiponectin 7 5 SZ Deltagen and Lexicon Knoc in the hypothalamus PMID 18394428 F dm Edn1 FEBS letters 2008 Apr 30 7 a Amh AdipoR 1 mediates the anorexigenic and insulin ictnJike actions of adiponectin in the hypothalamus 7 am Mapks 7m Agrp im Adipor1 adiponectin receptor 1 references MGI 1919924 CAGE Mm 1 136231891 E in Adipog adiponectin C1Q and collagen domain containing references MGI 106675 CAGE 7 iig Lepr Mm 16 23061870 23073302 Ia Nr3c1 in Lep leptin references MGI 104663 CAGE Mm 6 29010231 29023886 tS FS Documents section diseases box 13 Copyright 2005 2009 RIKEN 5 2 1 Hit and related molecules tabs These tabs display the descriptions of hit molecules Adipor1 etc related molecules Adipoq etc and their relationships Click a tab to display each description and change information of the related molecules and disease box and the documents section respectively ri lt Relation CETT d Adipor cio a dm ACAPORCI adiponectin receptor 1 HGNC 2 HMO CAGE Hic T221175575 201194023 eee Locus im aapi adiponectin receptor 1 172 references MoLT 19924 CAGE MmcT 12523 18091 13524 748 Rad L
21. m Tnnt2 E im Ctse a Sox13 E dm Ugtiat E de scr E Pam E ia Nr5a2 7 dm Bok E dap Ugt1a6a ag Acmsd F ag Ren2 Am Kiss1 E Trpm8 E ip Fmod 7 dm Ugt1a9 7 Im Ikbke 7 dm Avprib 7 4m ciz im Btg2 dm Rabif E dm Serpinbs 7 im 120 F aig Ren1 7 dm Miph The hit list box Pos to 140M clear version NCBIM36 gt condition genomic interval v species mouse Search condition J section All Hits Total Hits 114 3 747 sec Simple Mode mouse mutant HsPPI human gene record MEDLINE sentence mouse gene record OMIM REACTOME rat gene record Display condition e Associate the keyword with entities co cited within the same sentences v section Further associate the entities with entities co cited within the same sentences v Page 1 next display mode Simple v Insig2 insulin induced gene 2 im insig 26 docs Position Mm 1 123131899 123155308 Link to MGI T 4 S7 21 hits diabetes OR insulin CAGE 1110 interleukin 10 im mo 20845 docs Pvalue 106E 3417 Position Mm 1 132847393 132852516 Linkto MGI 4 s899 docs Pvalue 1 06E 3417 lm Tnf 94466 docs Position Mm 17 34807442 34810048 Linkto MGI S7 3871hits P value 2 96E 4095 diabetes OR insulin CAGE CAGE Se im Serpinb2 828 docs Pvalue 339E 1149 Position Mm 1 109338970 109353139 Linkto MGI 4712 d
22. me sentences Further associate the entities with entities ca cited within the same document Further associate the entities with none January 5th 2009 Copyright O 2005 2009 RIKEN 5 Set as target button to set them as the next search targets 6 Download button to download all hits as an Excel file 7 Draw button to draw the co citation networks of hit entries in another window All Hits Total Hits 50 4 805 sec Simple Mode mouse mutant human gene record MEDLINE sentence mouse gene record 1 im i51 OMIM PPI REACTOME rat gene record 2 7 in Capn10 Associate the keyword with entities co cited within the same sentences v 3 V dm Inpp5d N Further associate the entities with entities co cited within the same sentences v 4 im Psmd1 ee 1 next display mode Simple v http omicspace riken jp PosMed Positional MEDLINE Internet Explorer ln Lodo Ugtla9 L fial Ugtlldgel a2 R SPERENEULE J EEAS h REER 83 8 Page entry box and link to next previous page January 5th 2009 Copyright 2005 2009 RIKEN 9 Search result display mode mentioned in next section Simple display mode shows a compact list of the search results with minimum information Each result indicates the search path from keyword bottom to gene top 6 Adiporl1 adiponectin receptor 1 im Adipori 172 docs Pvalue 182E 499 Position Mm 1 136231891 136248
23. ment database containing MEDLINE abstracts etc by using arbitrary keywords users have entered And second PosMed finds significant gene names or symbols that exist within the returned documents with Fisher s exact test and makes a ranked list in this case significant means that the P value is as small as possible In the case where a user specifies the chromosomal interval PosMed makes and displays a ranked list of genes restricted to the given interval That is to say PosMed can search the connection of Keyword gt Gene A gt Chromosomal interval Simultaneously PosMed can also search for appropriate genes within the chromosomal interval that have an estimated gene gene interaction automatically The selected genes will fulfill the conditions of network connections of Keyword gt Gene B gt Gene C gt Chromosomal interval PosMed is a powerful tool which enables us to connect phenotypic functions and genes because it uses relevant information of not only gene gene interactions but also other biological objects interactions cell gene metabolite gene mutant mouse gene drug gene disease gene protein protein interaction and ortholog data PosMed enables us to search human and mouse genes drugs diseases and document sets e g MEDLINE and OMIM search gene condition genomic interval species mouse Pos Med Select Interval with OmicBrowse chromosome all gt position from T clear version NCBIm36 keyword
24. notypic Allele Detail Adipoqt 1Tka Adipoq adiponectin C1Q and collagen domain containing BRM 0007830 v MGI Phenotypic Allele Detail Adipogt 1 Ts Adipoq adiponectin C1Q and collagen domain containing references BRM 0007830 Mm 16 23061870 23073302 Mm 16 23061870 23073302 15 Copyright O 2005 2009 RIKEN 5 2 3 Related molecules and diseases box Other related molecules or diseases are listed as images in the left yellow box If the documents contain the keywords the related objects will be displayed with hit images e You can click a name e g Adipor2 to display the relationships document digests that include the keywords diabetes or insulin the gene name Adipor1 etc and the biological object e g Adipor2 etc in the documents section This function is the same as the Hit and related molecules tabs described previously DES Relation All Hits in Adipor1 ig Adipor2 i lt gt show graph P value 2 18E 1162 128 a 95 mouse mutant 0 HsPPI 0 MEDLINE 128 mouse gene record 0 REACTOME 0 Symbol Adipor1 Name adiponectin receptor 1 ID MGI 1919924 Link to MGI CAGE Position Mm 1 136231891 136248748 show graph Symbol Adipor2 Name adiponectin receptor 2 Other aliases D6Ucla1e ID MGI 93830 Link to MGI CAGE Position Mm 6 119318769 119383102 all 95 128 HsPPI 0 0 Adipor1 related entities keyword diabetes OR insulin year all
25. ocs Pvalue 339E 1149 i Serpine1 5879 docs Position Mm 5 137346135 137356886 Link to MGI S2 1222hits P value 2 04E 1293 diabetes OR insulin inb2 serine or cysteine peptidase inhibitor clade B member 2 CAGE CAGE Adora1 adenosine A1 receptor Adora1 72755docs Pvalue 5 18E 1062 Position Mm 1 136015644 136050989 Linkto MGI 4310 docs P value 5 18E 1062 Adenosine 7118618 docs Link to Original 4 1279 hits P value 1 09E 1353 diabetes OR insulin CAGE A list of the candidate genes v0 c fom e C im Ptprc 8068 docs Pvalue 485E 694 Position Mm 1 139879826 139991666 Linkto MGI 4 51500 docs Pvalue 4 85E 694 im Cd4 71180 docs Position 11m 6 124830325 124853807 Linkto MGI S7 685hits P value 1 44E 725 diabetes OR insulin rc protein tyrosine phosphatase receptor CAGE CAGE Adipor1 adiponectin receptor 1 im Adipori 172docs Pvalue 1 82E 499 Position Mm 1 136231891 136248748 Linkto MGI 244 docs Pvalue 1 82E 499 im Adipoq 3773 docs Position Mm 16 23061870 23073302 Link to MGI SX 4378hits P value 2 49E 4632 diabetes OR insulin CAGE CAGE Cxcr4 chemokine C X C motif receptor 4 Cxcr4 2751 docs Pvalue 424E 451 Position 1m 1 130415745 130419836 Link to 439 docs Pvalue 128E 535 Factor1 9033 docs Link to Original S 425 hits P value 4 24E 451 di
26. ocus dm Aper pdiponache recopier 14 ROO Er 131 47358524 4737 9554 pas Fl ii v apos errr 1808 1MMD ee DHI DHG IM cB pubis abun Da Apr Lior Fl nonsnsutn dependentia show GPA onder by fact draia E ln Vr aora 20 of 172 Faga 1 Fl dS pon PP camila imm adiponectin ceptor genes ADIPOR1 and ADIPOR E icon E Obesity nedes an oficial journal of fhe Inlemabienal Associaton bor the Study of Obesity 2007 Sep Li Ag AB Fuss Adqpenecto plas am important role in ngulin sensit via md and 2 e agna E iso IENFTTEEEN MAA LOCI m ADIPOO adipceaclin C10 and collagen domain containing HGNC 13523 CAGE Had 188043 155 199058345 Lock im ipod adiponectin 10 and collagen domain containing 2773 references WG 105575 CAGE Mm 16 2396 1870 Adipor related entites keyword dabei OF insin yer all any Ep i MEC El check ai i ne s i l igs sd m Lo M H E im v Adipog eine 1934 De idi ee 204 i4 2089 oe ODT 24d I im per putibcatign ye ar Fin nonansuin depend n da sey does darey ad dowmload Fd wr agon FD DengeaniledconEne 1 E Adiponectin and risk of coronary heart disease in older men and women F1 meant mnnn Fh sore of cnc qeesocrinolegy and malign 2008 Sap F dm c AB Fuse RESULTS Adiponectin exhibited significant negate correlations with baseline adipodity DOR insulin resisizace dyshipidemia inflammatory markers and pi January 5th 2009 14 Adipoq Hame ripiega C
27. por1 related entities keyword diabetes OR insulin year all v Find any a 1000 n 800 check all E 600 et as target S 400 Wi with keyword Find 200 A Bi without keyword NEM E B L end 7 in Adipoq 0 unknown 1999 2000 2001 2002 2003 2004 2005 2006 2007 2008 A fa Adipor2 publication year u TES V 7 non insulin dependent dia show digest order by fact 7 4 v Adipor1 S Deltagen and Lexicon Knoc 1 wv Adiponectin and risk of coronary heart disease in older men and women Ees PMID 18593765 The Journal of clinical endocrinology and metabolism 2008 Sep 7 ig Amh AB F ii Mapke RESULTS Adiponectin exhibited significant negative correlations with baseline adiposity ei insulin resistance dyslipidemia inflammatory markers and leptin im Aarp iip Map2k1 yn lm Le pr Rougnon Heberden disease references all 3038 3773 Adipor1 related entities via mouse mutant any E check all 2 Find 7 ig Sv ADIPOR1 7 E Adipor1 7 Y w Deltagen and Lexicon Knoc January 5th 2009 Mbhalaatacal FL rafarananaa UWIPVONNNANIL AOL mouse gene record 0 1 REACTOME other f databases 0 0 9 Fin keyword diabetes OR insulin year all v 2 d 10 AB v 6 E e 4 Bi with keyword 2 B Bi without keyword 0 P unknown 1999 2000 2001 2002 2003 2004 2005 2006 2007 2008 publication year show digest v order by fact 1 4 of 4 1 MGI Phe
28. s Total Hits 50 5 05sec ExpertMode v Neural weight for inferential search 7 hits v h dat mouse gene PP weak keyword diabetes OR insulin REACTOME weak v mouse mutant weak v mouse generecord Strong v MEDLINE sentence weak v 2 hits A keyword diabetes OR insulin 2 im mouse gene Homologue im human gene human gene record PPI weak v REACTOME weak OMIM weak v B dag mouse gene Homologue Iz rat locus ratgene record strong v keyword diabetes OR insulin 4 ap mouse gene mouse mutant mouse mutant mouse mutant strong v keyword diabetes OR insulin 4 Association pull down menu As above PosMed can search the connection of Keyword gt Gene A gt Gene B gt Chromosomal interval User can select the association status between the keyword and a single entity gene A etc or two entities The association status has can be set to either co cited within the same sentences or documents 4 1 represents the association status between the keyword and Gene A The default is set to the association of entities co cited within the same sentences Associate the keyword with entities co cited within the same sentences Associate the keyword with entities co cited within the same document 4 2 represents the association status between Gene A and Gene B The default is set to the association of none Further associate the entities with entities co cited within the sa
29. ue Gene position link Link to original to OmicBrowse database Number of documents Link to display CAGE describing the gene data in OmicBrowse 10 January 5th 2009 Copyright O 2005 2009 RIKEN 4 2 Relationship displayed in the Tree mode In the Tree mode the hierarchy structure indicates the search path from keywords bottom to genes top in much the same way as the Simple mode 5 Adipori adiponectin receptor 1 im Adipor1 1172 docs Pvalue 1 82E 499 Position Mm 1 136231891 136248748 Linkto MGI CAGE L 244 docs Pvalue 1 82E 499 Lim Adipog 13773 docs Position Mm 16 23061870 23073302 Linkto MGI CAGE L sz 4378 hits P value 2495 4632 L diabetes OR insulin 4 3 Relationship displayed in the Graph mode In the Graph mode each result indicates the search path from keywords right to genes left Rank order Gene symbol and name Gene corresponding to the search conditions 6 Adipor1 adiponectin receptor 1 Interval Mouse Locus Co citation Mouse Locus Keyword lt gt i show graph Rif E show graph t Symbol Adipor1 P t 1 82E 499 Symbol Adipoq P value 2 49E 4632 Name adiponectin receptor 1 244 Name adiponectin C1Q and collagen P value 1 82E 499 domain containing ID MGI 1919924 set as target Other aliases adipoQ adiponectin 172 GBP28 apM1 adipo Acrp30 Acdc MGI CAGE ID MGI 106675 Mm 1 136231891 136248748 3 3773 Number of do
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