GeneSpider User Manual - research.dfci.harvard.edu
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1. protein Tapetochoroidal Dystrophy TCD AC004386 HTG AC004388 HTG Z98950 dJ507115 1 match multiple match multiple proteins match 60S ribosomal L36 L41 proteins match CE02123 P90702 Q96499 P10661 L44 Xq26 3 27 3 CE02123 P90702 P65027 match P09896 P31866 Q96499 P10661 P02405 P31028 P52809 match P65027 match Q00477 Q00494 P49213 P17843 P09896 P31866 P27076 match cDNAs M19635 P02405 P31028 M15661 AB000910 match multiple P52809 match ESTs match T87328 T87321 Q00477 Q00494 AA181201 T41136 match AA244162 P49213 P17843 R05264 N93353 AA191627 match P27076 match AA411822 AA328207 AA342359 cDNAs M19635 T89286 60S ribosomal protein L44 M15661 L41 L36 like AB000910 match multiple ESTs match T87328 T87321 AA181201 T41136 match AA244162 R05264 N93353 AA191627 match AA411822 AA328207 AA342359 T89286 60S ribosomal protein L44 L41 L36 like AC004478 HTG AC003666 HTG AC002549 HTG AC003669 HTG Z82204 repeat polymorphism X AC004383 HTG Copyright Silicon Genetics 2000 13 The GeneSpider AC004072 HTG AC003683 HTG AC003658 HTG Y15994 MTM1 gene AL009175 REP1 Imatch SW dA43C13 1 RAB PROTEINS Ichoroideremia rab P24386 EMBL GERANYLGERANYLTRANSFERASE geranylgerany transferase X78121 RAB COMPONEN2. REP1 Tapetochoroidal Dystrophy TCD AC004386 HTG AC004388 HTG Z98950 dJ507I15 1 match multiple proteins match CE02123 P90702 Q96499 P10661 P65027 match P09896 P31866 P02405 P31028 P52809 match Q00477 Q00494 P49213 P17843 P27076 match cDNAs M19635 M15661 AB000910 match multiple ESTs match T87328 T87321 AA181201 T41136 match AA244162 R05264 N93353 AA191627 match AA411822 AA328207 AA342359 T89286 60S ribosomal protein L44 L41 L36 like 60S ribosomal L36 L41 L44 Xq26 3 27 3 AC004478 HTG AC003666 HTG AC002549 HTG AC003669 HTG Z82204 repeat polymorphism X AC004383 HTG Copyright Silicon Genetics 2000 11 The GeneSpider AC004072 HTG AC003683 HTG AC003658 HTG Y15994 MTM1 gene AL009175 REP1 match SW P24386 EMBL X78121 RAB ESCORT PROTEIN 1 REP 1 CHOROIDERAEMIA PROTEIN TCD PROTEIN dA43C13 1 RAB PROTEINS GERANYLGERANYLTRANSFERASE COMPONENT A 1 choroideremia rab geranylgeranyl transferase Xq21 1 Xq21 3 AC003037 HTG AL008713 steroid 5 alpha reductase match M32313 dJ93C23 1 3 oxo 5 alpha steroid delta 4 dehydrogenase dihydrotestosterone pseudogene X AC002422 HTG AC002523 HTG M22332 ORF putative unknown protein L1 insertion element AQ409366 GSS AQ356884 GSS AQ309743 GSS X61295 L1 retroposon a portion of its ORF2 sequence L1 retroposon reverse transcriptase like protein AQ572229 GSS A1683867 EST AQ390430 GSS AQ355719 GSS AQ559819 GSS AQ557343 GSS AQ573089 GSS M549
3. 15 o GSS AQ344044 o GSS AQ378406 ai GSS U70924 _ reverse transcriptase Z78996 Anonymous marker single read J00338 sid repeat region AQ547459 al GSS Figure 14 The same file as illustrated in Figure 13 shown in Excel format The first row of column headings is not automatically included in new gene list files they have been added here for clarity Copyright Silicon Genetics 2000 15
4. 85 psi eta beta like globin pseudogene AQ549999 GSS AI421777 EST AQ420901 GSS AQ382430 GSS AQ440210 GSS AQ536099 GSS AI475350 EST 67068 AI821169 EST AL045241 EST AQ357079 GSS S80119 reverse transcriptase homolog This sequence comes from Fig 2 Protein sequence is in conflict with the conceptual translation X61294 L1 retroposon a portion of its ORF2 sequence L1 retroposon reverse transcriptase like protein AQ377979 GSS AQ342069 GSS K02590 pseudo h3 pseudo beta globin beta globin h3 globin pseudogene AQ545809 GSS Z96215 genomic fragment subtelomeric DNA AQ572877 GSS AQ554929 GSS AQ545915 GSS AQ344044 GSS AQ378406 GSS U70924 reverse transcriptase Copyright Silicon Genetics 2000 12 The GeneSpider Z78996 Anonymous marker single read J00338 repeat region AQ547459 GSS Figure 13 The updated version of the file illustrated in Figure 3 Systematic Common Map EC Description Product ie can Keywords GenBank Name Name Number locus 297181 1 HTG DXS7 GT repeat polymorphism GTG repeat polymorphism AL022401 CHM 5 part of gene dJ93L7 1 RAB Escort protein 1 HTG CHM beyond this clone REP 1 RAB proteins Choroideraemia match proteins _ geranylgeranyltransferase component geranylgeranyltransferase P24386 P37727 JA 1 Choroideraemia protein component A 1 RAB P26374 Tapetochoroidal Dystrophy TCD Escort REP 1 REP1
5. GeneSpider User Manual Release Date 17 April 2000 Copyright 2000 Silicon Genetics All rights reserved GeneSpring GeneSpider GenEx and MicroSift are trademarks of Silicon Genetics All other products including but not limited to GeneBank Microsoft Excel Microsoft Notepad and Adobe FrameMaker are the trademarks of their respective holders Copyright Silicon Genetics 2000 The GeneSpider Table of Contents Chapter 1 TheGe eneSpidefensicenirinsianoninogi rn e a nas acon tdaaniiaataare 3 1 1 What does the GeneSpider dO isis sss siccusenavetwosd genes caaasniessivynshsnagsstusdeapeatsansseteurveye 3 1 2 What data do you need to use the GeneSpider ee eeeeeesneeceeeeeeeeeesenteeeeeeeees 3 1 2 1 The GeneSpider file format css seseterieiririesesin mi orani ei 3 eS RUMI the GeneSpidet ie rnesa a a a eaa aae oa 6 1 3 1 To add or update the information associated with each GenBank ACCESSION MUMDET 2 seii eo nes niis eanas inasra raai behead betes stecdaves 6 Copyright Silicon Genetics 2000 2 The GeneSpider Chapter 1 The GeneSpider 1 1 What does the GeneSpider do Given a list of GenBank accession numbers the GeneSpider searches either GenBank or Locus Link for information associated with those accession numbers and caches it for your future use Searching Locus Link is currently only useful for human genes 1 2 What data do you need to use the GeneSpider To use the GeneSpider you need a list of GenBank a
6. T A 1 Xq21 1 Xq21 3 ESCORT PROTEIN 1 REP 1 CHOROIDERAE MIA PROTEIN TCD PROTEIN AC003037 HTG AL008713 steroid 5 alpha dJ93C23 1 3 oxo 5 alpha steroid reductase match delta 4 dehydrogenase M32313 dihydrotestosterone pseudogene X AC002422 HTG AC002523 HTG M22332 ORF putative lunknown L1 insertion element protein AQ409366 GSS AQ356884 GSS AQ309743 GSS X61295 L1 retroposon a portion of its ORF2 sequence L1 retroposon reverse transcriptase like protein AQ572229 GSS Al683867 EST AQ390430 GSS AQ355719 GSS AQ559819 GSS AQ557343 GSS AQ573089 GSS M54985 ipsi eta beta like globin pseudogene AQ549999 IGSS Al421777 EST AQ420901 GSS AQ382430 GSS AQ440210 GSS AQ536099 GSS Al475350 EST 567068 Al821169 EST AL045241 EST AQ357079 GSS 80119 reverse transcriptase This sequence comes from Fig 2 Protein sequence is in conflict with the conceptual homolog translation Copyright Silicon Genetics 2000 14 The GeneSpider X61294 L1 retroposon a portion of its ORF2 sequence L1 retroposon reverse transcriptase like protein AQ377979 o GSS AQ342069 O GSS IK02590 pseudo h3 pseudo beta globin beta globin h3 globin pseudogene AQ545809 GSS Z96215 genomic fragment subtelomeric DNA AQ572877 ea GSS AQ554929 m GSS AQ5459
7. ccession numbers these are also known as GenBank identifiers or the GenBank locus In addition you may also have alternative names functional information map positions EC numbers and so on associated with each gene This information should be saved in the same file using GeneSpider file format described below Hereafter the file containing this information will be referred to as the gene list file The gene list file must be a tab delineated text file When saving their gene list files Windows users should look for the document type Text Tab delimited txt in the Save as type dialog box The gene list file may be created in a spreadsheet program such as Microsoft Excel if it is saved as a tab delineated text file 1 2 1 The GeneSpider file format The GeneSpider file format is a tab delimited text file consisting of one line per gene with several fields separated by tabs The first field systematic name must be included for every gene the other nine fields are optional but must be entered in the order presented here 1 Systematic Name The normal way of referring to this gene This name must be unique and every gene must have one Frequently the name used in this column is the gene s GenBank accession number otherwise it may be the name which labels the gene s raw signal strength values in your array or other experimental data files it may be the gene s location on the array or it may be any other uniqu
8. e identifier you wish associated with each gene This column must be included in your gene list file and it must be filled for every gene 2 Common Name An alternative way of referring to this gene Genes are not required to have a common name and common names do not have to be unique This column may contain the GenBank accession numbers 3 Map Mapping information for this gene For example 16q12 1 or 123 358 if the full nucleotide sequence is known for your organism 4 EC number The EC number for this gene 5 Description A description of this gene Copyright Silicon Genetics 2000 3 The GeneSpider 6 Product What this gene produces 7 Phenotype A description of the phenotype for this gene 8 Function A description of the function of this gene 9 Keywords Keywords associated with this gene 10 GenBank locus The GenBank accession number for this gene If the GenBank identifiers for your genes were not used as either their systematic or common names then they must be included in this field When creating your gene list file these ten fields should be entered in the order they are listed here Remember to include any blank fields in their appropriate columns The gene s systematic name should always be in the first column its common name is in the second and its mapping information in the third column even if the second column is completely blank because there are no common names for any of your genes F
9. eneSpider c 1999 Silicon Genetics of x GeneSpider allows you to extract some information from GenBank for a series of genes You must give GeneSpider a file containing a list of the genes Please enter the filename below File Name D GeneSpider Genes tat Bias Database to search GenBank OK Cancel Help Copyright Silicon Genetics 2000 The GeneSpider Figure 7 The initial GeneSpider window with a file indicated in the File Name box 4 Click the arrow at the right hand corner of the box labeled Database to search This opens a pull down menu Figure 8 The Databases to search menu 5 Choose which database you wish to search by clicking it The name of the database you will be searching should now be in the Database to search box 6 Click the OK button The GeneSpider window will change Update Genome Genes txt by GenBank iof x Options Use for GenBank identifier Column 1 Systematic Name I Overwrite existing information Status Processed 0 Found 0 Enhanced 0 ToGo O Waiting to start Save gene list to DAG eneS pider Genes txt Start Stop Gave and clase Figure 9 The second GeneSpider window the Update Genome from GenBank window 7 Click the arrow to the right of the box labeled Use for GenBank identifier This opens a pull down menu Column 10 GenBank Locus Column 1 Systematic Name Column 2 Co
10. in the GeneSpider window reflecting the information it has processed After the gene list file has been updated you are given the option to permanently save the updated information When you save this information it is saved in the GeneSpider format tab delimited text file in the same directory as your original gene list file You may then open this text file using a spreadsheet program such as Microsoft Excel The updated file is saved in the GeneSpider format so the next time you wish to update the information associated with your set of genes you can use this new file as the initial gene list file 1 3 1 To add or update the information associated with each GenBank accession number 1 Create your gene list file Z97181 1 AL022401 AC004386 AC004388 Z98950 AC004478 AC003666 AC002549 AC003669 Z82204 AC004383 AC004072 AC003683 AC003658 Y15994 AL009175 AC003037 AL008713 AC002422 AC002523 M22332 AQ409366 AQ356884 AQ309743 X61295 AQ572229 AI683867 AQ390430 AQ355719 Copyright Silicon Genetics 2000 6 The GeneSpider AQ559819 AQ557343 AQ573089 M54985 AQ549999 AI421777 AQ420901 AQ382430 AQ440210 AQ536099 AI475350 S67068 AI821169 AL045241 AQ357079 S80119 X61294 AQ377979 AQ342069 K02590 AQ545809 Z96215 AQ572877 AQ554929 AQ545915 AQ344044 AQ378406 U70924 Z78996 J00338 AQ547459 Figure 3 Example GeneSpider gene list file The only column required in the gene list file is s
11. it does not find anything it will copy any information you already had about that gene into the new file it is creating and go on to the next gene Copyright Silicon Genetics 2000 4 The GeneSpider Systematic Common Map EC Number Description Product Phenotype Function Keywords GenBank locus Name Name gene 1 luck1 1 1 1 1 gene somehow _proteinA g763402 causes rats to be very lucky gene 2 16q21 2 1 1 1 2 co produces protein B g764509 gene 3 1 1 1 3 g587439 gene 4 1 1 1 4 deletion causes immortality g093285 gene 5 1 1 1 5 9460389 gene 6 charm5 15q42 3 1 1 1 6 rats with this protein C cell cycle g932509 gene are very cute gene 7 1 1 1 7 g328506 gene 8 9q11 0 1 1 1 8 protein D possibly 9234876 gene 9 beauty3 16q14 1 1 1 1 9 involved in metabolism metabolism gene 9 5 19q76 7 1 1 2 0 protein D possibly 9239857 gene 10 1 1 2 1 9238456 gene 10 2 possibly a mutation gene 11 1 1 2 2 9239845 gene 12 weird2 16q44 2 1 1 2 3 rats with this protein E involved in IDNA g290030 gene have two DNA synthesis tails synthesis gene 13 16q87 9 1 1 2 4 protein F g321197 gene 14 Figure 1 Example of what the GeneSpider format looks like in Excel Systematic Name Common Name Map EC Number Description Product Phenotype FunctionKeywords GenBank locus gene 1 luckl 1 1 1 1 gene somehow causes rats to be very lucky protein A g763402 ge
12. mmon Name Figure 10 The Use for GenBank identifier menu 8 Click the column in your gene list file containing the GenBank accession numbers Copyright Silicon Genetics 2000 9 The GeneSpider 9 If you have information beyond the GenBank accession number in your gene list file the Overwrite existing information checkbox pertains to you If you select the checkbox you tell the Spider to overwrite any information already in your gene list file if it finds similar information for that gene on the web If you do not select in the Overwrite existing information checkbox any information about the genes already in your gene list file will not be modified or updated by information from the web 10 Click the Start button The Spider will process the data from the web displaying how far it has gotten in the box labeled Status This search may take awhile When you are updating long lists of genes it is better to leave this process running overnight as it may take a few hours Messages saying the Spider is caching information may appear during this process Update Genome Genes txt by GenBank iof x Options Use for GenBank identifier Column 1 Systematic Name P Overwrite existing information Status Processed 5 Found 4 Enhanced 4 56 Processing gene 298950 Save gene list to DAG eneS pider Genes txt Start Stop Save and clase Figure 11 The Update Genome from Ge
13. nBank window during the search of GenBank Copyright Silicon Genetics 2000 10 The GeneSpider Update Genome Genes txt by GenBank Iof x Options Use for GenBank identifier Column 1 Systematic Name x I Overwrite existing information Status Processed 61 Found 60 Enhanced 59 ToGo 0 Done but not Saved Save gene list to DAG eneSpider Genes txt Start Stop Save and close Figure 12 The Update Genome from GenBank window after the GenBank search is complete 11 Write the name you would like the updated gene list saved as in the box labeled Save gene list to If you are a Windows user remember to include the txt suffix The updated gene list file will be saved in the same directory as the original gene list file unless you type a different pathway in this box 12 Click the Save and close button to save the updated gene list file This also closes the GeneSpider 13 The file resulting from the search illustrated in this document is illustrated in Figure 13 and Figure 14 Z97181 HTG DXS7 GT repeat polymorphism GTG repeat polymorphism AL022401 CHM 5 part of gene beyond this clone match proteins P24386 P37727 P26374 dJ93L7 1 RAB Escort protein 1 REP 1 RAB proteins geranylgeranyltransferase component A 1 Choroideraemia protein Tapetochoroidal Dystrophy TCD protein HTG CHM Choroideraemia geranylgeranyltransferase component A 1 RAB Escort REP 1
14. ne 2 16q21 2 1 1 1 2 co produces protein B g764509 gene 3 1 1 1 3 g587439 gene 4 1 1 1 4 deletion causes immortality g093285 gene 5 1 1 1 5 g460389 gene 6 charm5 15q42 3 1 1 1 6 rats with this gene are very cute protein C cell cycle g932509 gene 7 1 1 1 7 g328506 gene 8 9q11 0 1 1 1 8 protein D possibly g234876 gene 9 beauty3 16q14 1 1 1 1 9 involved in metabolism metabolism gene 9 5 19q76 7 1 1 2 0 protein D possibly g239857 gene 10 1 1 2 1 g238456 gene 10 2 possibly a mutation gene 11 1 1 2 2 g239845 gene 12 weird2 16q44 2 1 1 2 3 rats with this gene have two tails protein E involved in DNA synthesisDNA synthesis g290030 gene 13 16q87 9 1 1 2 4 protein F g321197 gene 14 Figure 2 Example of the same GeneSpider file shown in Figure 1 saved as a tab delimited text file Copyright Silicon Genetics 2000 5 The GeneSpider 1 3 Running the GeneSpider The accession numbers must be included in the gene list file in one of three columns as the genes systematic name common name or as the entry in the GenBank locus field Do not worry if your gene list file includes genes without GenBank accession numbers When you update a gene list file using the GeneSpider the Spider copies your current gene list file so you do not loose any information regarding non GenBank genes After the GeneSpider copies this file it updates the fields of the copied file associated with a GenBank accession number While it is copying and updating you will see changes
15. requently only the first field systematic name is used in the gene list file in this case it must contain the genes GenBank accession numbers If you do this your file will be similar to the one illustrated in Figure 3 page 7 Otherwise your gene list file should resemble the file illustrated in Figure 1 and Figure 2 Entries with spaces in them such as Gene 1 are perfectly acceptable Each field must be separated from the next one by a tab character You do not need to have information about every gene In the example below nothing is known about Gene 14 so the line after its name is left blank If you have a list of genes and text information about them in a spreadsheet formatted as ten columns with one row per gene simply save this file as a tab delineated text file A note about the figures do not include the titles of the fields in your gene list file titles are included here only for clarity The GenBank accession numbers are the only information absolutely necessary to include in the gene list file They may be included as the systematic name the common name or as the GenBank locus All of the GenBank accession numbers for your genes must be included in the same column If that column is either the systematic name column or the common name column then not every entry in that column must be a GenBank accession number The GeneSpider will search GenBank for every name given in the column containing the GenBank accession numbers if
16. ystematic name column if it contains the GenBank accession number for each gene This is the simplest gene list file to create 2 Click the GeneSpider icon to bring up the first GeneSpider window S GeneS pider Figure 4 The GeneSpider icon Copyright Silicon Genetics 2000 The GeneSpider GeneSpider c 1999 Silicon Genetics Ioj Xx GeneSpider allows you to extract some information from GenBank for a series of genes You must give GeneSpider a file containing a list of the genes Please enter the filename below File Name Browse Database to search GenBank OK Cancel Help Figure 5 The initial GeneSpider window 3 In the first box labeled File Name enter the complete file name and the pathway of your gene list file If you are a windows user be sure to include the txt suffix To enter this information either write the complete directory pathway in the File Name box or a Click the Browse button A browse window appears in an oi e GIRE PAIHGING E gerwansy tat E becuase 4 f F nt ot bp irer 4 Cae Figure 6 The Browse directory b Find your gene list file c Select your gene list file by clicking it This will enter the gene list file name in the File name box of the Browse window d Click the Open button This writes the complete file name and pathway in the File Name box in the GeneSpider window G
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