========================================================================== TABLE OF CONTENTS ========================================================================== 1. TIGR Gene Index 3.0 release Statistics 2. Methodology 3. Output Data 4. File Format 5. Contacts ========================================================================== 1. TIGR Gene Index 3.0 release Statistics Gene Ontology Gene Associations (species and # assignments) are provided for the following TIGR Gene Index (TGI) divisions (http://www.tigr.org/tdb/tgi.shtml): taxon_id --------- Animals: Amblyomma variegatum 296 34610 Salmo salar 3018 8030 Brugia malayi 1089 6279 Ictalurus punctatus 1457 7998 Bos taurus 11717 9913 Caenorhabditis elegans 6343 6239 Canis familiaris 2002 9615 Gallus gallus 12777 9031 Ciona intestinalis 5347 7719 Drosophila melanogaster 28566 7227 Apis mellifera 889 7460 Homo sapiens 64898 9606 Anopheles gambiae 12953 7165 Mus musculus 50036 10090 Oryzias latipes 5888 8090 Onchocerca volvulus 467 6282 Sus scrofa 6394 9823 Rattus norvegicus 20423 10116 Oncorhynchus mykiss 7475 8022 Schistosoma mansoni 634 6183 Xenopus laevis 12507 8355 Danio rerio 9938 7955 Plants: Arabidopsis thaliana 13974 3702 Hordeum vulgare 8365 4513 Chlamydomonas reinhardtii 1465 3055 Gossypium 3057 3633 Vitis vinifera 3174 29760 Mesembryanthemum crystallinum 1471 3544 Lactuca sativa 1689 4236 Lotus japonicus 1303 34305 Zea mays 6346 4577 Medicago truncatula 7035 3880 Pinus 3201 3337 Solanum tuberosum 5244 4113 Oryza sativa 7360 4530 Secale cereale 628 4550 Sorghum bicolor 2860 4558 Glycine max 8912 3847 Helianthus annuus 1081 4232 Lycopersicon esculentum 5896 4081 Triticum aestivum 7824 4565 Protists: Cryptosporidium parvum 150 5807 Dictyostelium discoideum 1218 44689 Eimeria tenella 223 5802 Leishmania 201 5658 Neospora caninum 251 29176 Plasmodium berghei 323 5821 Plasmodium falciparum 1081 5833 Plasmodium yoelii 747 5861 Sarcocystis neurona 307 42890 Trypanosoma brucei 357 5691 Trypanosoma cruzi 286 5693 Toxoplasma gondii 846 5811 Tetrahymena thermophila 155 5911 Fungi: Aspergillus nidulans 669 5072 Coccidioides immitis 245 5501 Filobasidiella neoformans 2192 5207 Magnaporthe grisea 1309 148305 Neurospora crassa 251 5141 Saccharomyes cerevisiae 12996 4932 Schizosaccharomyces pombe 1703 4896 2. Methodology Using dps_btab, individual TC and NP sequences comprising each Gene Index Database were searched against a protein database consisting of FB,GOA_SPTR,GOA_human,GeneDB_Spombe, MGI,SGD,TAIR,TIGR_Ath1,TIGR_Pfa1 and WB sequences mapped to GO. 3. Output Data Gene Ontology Association were built utilizing the following files from Gene Ontology Consortium: gene_association.fb gene_association.goa_sptr gene_association.goa_human gene_association.GeneDB_Spombe gene_association.mgi gene_association.sgd gene_association.tair gene_association.tigr_ath gene_association.wb 4. File Format The file format follows the guidelines provided by the Gene Ontology Consortium (www.geneontology.com). 1. DB Database from which annotated entry has been taken. Here: Always 'TGI' for TIGR Gene Index. Example: TGI 2. DB_Object_ID A unique identifier in the DB for the item being annotated. Example: THC713899 3. DB_Object_Symbol A (unique and valid) symbol to which DB_Object_ID is matched. Here: Always the same as DB_Object_ID. Example: THC713899 4. NOT Here: Currently not applicable, always empty. 5. GOid The GO identifier for the term attributed to the DB_Object_ID. Example: GO:0005625 6. DB:Reference Reference cited to support the attribution. 7. Evidence Here always 'IEA'. Example: IEA 8. With Here: DB:gene_id 9. Aspect One of the three ontologies: P (biological process), F (molecular function) or C (cellular component). Example: P 10. DB_Object_Name Name of gene or gene product (as annotated by the participating protein database) 11. Synonym Gene Symbol [or other text] (as annotated by the participating protein database) 12. DB_Object_Type What kind of entity is being annotated. Here: always 'transcript' Example: transcript 13. Taxon_ID Identifier for the species being annotated. Here: One of 61 different TGI species. Example: taxon:9606 (human) 14. Date Date on which the annotation was made; format is YYYYMMDD Example: 20030601 15. Assigned_by The database which made the annotation. Here: Always 'TGI' for TIGR Gene Index. Example: TIGR_TGI 5. Contacts Please direct any questions to tgi_only@tigr.org.