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Re: [Gmod-gene-page] Unified Gene Page Comparison
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From: Michael T. <mt...@ta...> - 2005-02-03 10:42:10
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Vasanth - Great! except your url is for an ms word document. Could you post an html version? Cheers Mike Thon On Feb 2, 2005, at 6:05 PM, Vasanth Ragunathan Singan wrote: > Hi GMOD Gene Page group, > > Based on the suggestions from various members of this group, we at the > Genome Informatics lab have compiled a comparison with the GeneSummary > suggestions from Flybase. > > Attached is a HTML document of the comparison. > > The full documentation of this can be found at > http://eugenes.org:7072/all/gene-report-examples/doc/ > UnifiedGenePageCmp1.doc > > Looking forward for suggestions from you. > > thanks, > Vasanth > > > ---------------------------------- > Vasanth Singan > Graduate Research Assistant, > Genome Informatics Laboratory, > Indiana University - Bloomington > > vs...@in... > ---------------------------------- > <html> > > <head> > <meta http-equiv="Content-Type" content="text/html; > charset=windows-1252"> > <title>Following are the suggestions fr</title> > <style> > <!-- > p.MsoNormal > {mso-style-parent:""; > margin-bottom:.0001pt; > font-size:12.0pt; > font-family:"Times New Roman"; > margin-left:0in; margin-right:0in; margin-top:0in} > h2 > {margin-top:12.0pt; > margin-right:0in; > margin-bottom:3.0pt; > margin-left:0in; > page-break-after:avoid; > font-size:14.0pt; > font-family:Arial; > font-style:italic} > --> > </style> > </head> > > <body> > > <p class="MsoNormal">FlyBase suggested GeneSummary contents from > GeneSummary.dtd; > version 0.3; 12 Jun 2004,</p> > <p > class="MsoNormal"> http://eugenes.org/all/gene-report-examples/ > conf/GeneSummary.dtd</p> > <p class="MsoNormal"> </p> > <p class="MsoNormal">CATEGORIES</p> > <p class="MsoNormal"> BASIC_INFORMATION,</p> > <p class="MsoNormal"> LOCATION,</p> > <p class="MsoNormal"> GENE_PRODUCT,</p> > <p class="MsoNormal"> GENE_ONTOLOGY,</p> > <p class="MsoNormal"> SIMILAR_GENES,</p> > <p class="MsoNormal"> FUNCTION,</p> > <p class="MsoNormal"> REAGENTS,</p> > <p class="MsoNormal"> LITERATURE,</p> > <p class="MsoNormal"> SUMMARY,</p> > <p class="MsoNormal"> ADDITIONAL_INFORMATION</p> > <p class="MsoNormal"> </p> > <p class="MsoNormal">BASIC_INFORMATION = primary gene info </p> > <p class="MsoNormal"> Symbol </p> > <p class="MsoNormal"> Full_name </p> > <p class="MsoNormal"> Synonyms (text|Name)</p> > <p class="MsoNormal"> GeneID </p> > <p class="MsoNormal"> Species </p> > <p class="MsoNormal"> </p> > <p class="MsoNormal">LOCATION : location in genome</p> > <p class="MsoNormal"> Chromosome </p> > <p class="MsoNormal"> Scaffold </p> > <p class="MsoNormal"> Genome_map </p> > <p class="MsoNormal"> </p> > <p class="MsoNormal">GENE_PRODUCT : products of genes at sequence and > above > levels</p> > <p class="MsoNormal"> Polypeptides > (Polypeptide|Description|note)</p> > <p class="MsoNormal"> Transcripts > (Transcript|Description|note)</p> > <p class="MsoNormal"> Polypeptide (text|db_xref)</p> > <p class="MsoNormal"> Transcript > (text|Polypeptide|db_xref)</p> > <p class="MsoNormal"> Gene_type </p> > <p class="MsoNormal"> Sequence (text|db_xref)</p> > <p class="MsoNormal"> </p> > <p class="MsoNormal">GENE_ONTOLOGY : standardized GeneOntology.org > parts</p> > <p class="MsoNormal"> Molecular_function (text|goterm)</p> > <p class="MsoNormal"> Biological_process (text|goterm)</p> > <p class="MsoNormal"> Cellular_component (text|goterm)</p> > <p class="MsoNormal"> goevidence </p> > <p class="MsoNormal"> goterm (text|goevidence|ref)</p> > <p class="MsoNormal"> </p> > <p class="MsoNormal">FUNCTION : catch-all for higher level gene > actions; better > name?</p> > <p class="MsoNormal"> Protein_domains (db_xref|note)</p> > <p class="MsoNormal"> External_links (db_xref|url|note)</p> > <p class="MsoNormal"> Expressions (Expression|note)</p> > <p class="MsoNormal"> Expression (text|Phenotype)</p> > <p class="MsoNormal"> Phenotypes (Phenotype|note)</p> > <p class="MsoNormal"> Phenotype </p> > <p class="MsoNormal"> Interactions (Interaction|note)</p> > <p class="MsoNormal"> Interaction </p> > <p class="MsoNormal"> </p> > <p class="MsoNormal">REAGENTS : PCR, cDNA, EST, ... elements (REAGENTS > is used > now be a few MODs)</p> > <p class="MsoNormal"> Add an ALLELES/VARIANTS? > REAGENTS_AND_VARIANTS ?</p> > <p class="MsoNormal"> Reagent (text|db_xref|note)</p> > <p class="MsoNormal"> </p> > <p class="MsoNormal">SIMILAR_GENES : list of related organism genes, > probably > blast-computed from proteins</p> > <p class="MsoNormal"> (alternate names : similarities, > related_genes, homologs, > orthologs)</p> > <p class="MsoNormal"> Similarity > (Species|db_xref|Description|Symbol|Evalue|Percent)</p> > <p class="MsoNormal"> Evalue </p> > <p class="MsoNormal"> Percent </p> > <p class="MsoNormal"> </p> > <p class="MsoNormal"> </p> > <p class="MsoNormal">LITERATURE : relevant experimental references</p> > <p class="MsoNormal"> (alternate names : Bibliography, > References)</p> > <p class="MsoNormal"> Reference (text|ref|note)</p> > <p class="MsoNormal"> </p> > <p class="MsoNormal">SUMMARY : a human-readable text summary of gene > information</p> > <span style="font-size: 12.0pt; font-family: Times New > Roman"> SUMMARY (text|html)</span><p > class="MsoNormal"> </p> > <p class="MsoNormal">Following are the suggestions from various > members of the > working group and the above GeneSummary equivalents marked with > red.</p> > <p class="MsoNormal"> </p> > <h2>Arabidopsis</h2> > <pre style="font-size: 10.0pt; font-family: Courier New; margin-left: > 0in; margin-right: 0in; margin-top: 0in; margin-bottom: .0001pt">Locus > Info*</pre> > <pre style="font-size: 10.0pt; font-family: Courier New; margin-left: > 0in; margin-right: 0in; margin-top: 0in; margin-bottom: .0001pt"> > Systematic Locus Identifier* > <span style="color: red">BASIC_INFORMATION (GeneID)</span></pre> > <pre style="font-size: 10.0pt; font-family: Courier New; margin-left: > 0in; margin-right: 0in; margin-top: 0in; margin-bottom: .0001pt"> > Gene Name* <span style="color: > red">BASIC_INFORMATION (Full_name)</span></pre> > <pre style="font-size: 10.0pt; font-family: Courier New; margin-left: > 0in; margin-right: 0in; margin-top: 0in; margin-bottom: .0001pt"> > Gene Alias(es)* <span > style="color: red">BASIC_INFORMATION (Synonyms)</span></pre> > <pre style="font-size: 10.0pt; font-family: Courier New; margin-left: > 0in; margin-right: 0in; margin-top: 0in; margin-bottom: .0001pt"> > Gene Model Type (e.g. protein > coding, miRNA, unknown...etc.)*</pre> > <pre style="font-size: 10.0pt; font-family: Courier New; margin-left: > 0in; margin-right: 0in; margin-top: 0in; margin-bottom: > .0001pt"> <span > style="color: red">GENE_PRODUCT (GeneModel)</span></pre> > <pre style="font-size: 10.0pt; font-family: Courier New; margin-left: > 0in; margin-right: 0in; margin-top: 0in; margin-bottom: .0001pt"> > Physical/Genetic Linkage Map > Location (chromosome, coordinates)*</pre> > <pre style="font-size: 10.0pt; font-family: Courier New; margin-left: > 0in; margin-right: 0in; margin-top: 0in; margin-bottom: .0001pt"><span > style="color: red"> LOCATION > (Chromosome|Genome_map|Map)</span></pre> > <pre style="font-size: 10.0pt; font-family: Courier New; margin-left: > 0in; margin-right: 0in; margin-top: 0in; margin-bottom: .0001pt"> > Summary/Brief Description*</pre> > <pre style="font-size: 10.0pt; font-family: Courier New; margin-left: > 0in; margin-right: 0in; margin-top: 0in; margin-bottom: .0001pt"><span > style="color: red"> > SUMMARY</span></pre> > <pre style="font-size: 10.0pt; font-family: Courier New; margin-left: > 0in; margin-right: 0in; margin-top: 0in; margin-bottom: .0001pt"> > Annotated Sequence (gene features > annotated + EVIDENCE* that is</pre> > <pre style="font-size: 10.0pt; font-family: Courier New; margin-left: > 0in; margin-right: 0in; margin-top: 0in; margin-bottom: .0001pt"> -is > the structure experimentally verified or predicted and what is > the</pre> > <pre style="font-size: 10.0pt; font-family: Courier New; margin-left: > 0in; margin-right: 0in; margin-top: 0in; margin-bottom: .0001pt"> > evidence)</pre> > <pre style="font-size: 10.0pt; font-family: Courier New; margin-left: > 0in; margin-right: 0in; margin-top: 0in; margin-bottom: .0001pt"> > History</pre> > <pre style="font-size: 10.0pt; font-family: Courier New; margin-left: > 0in; margin-right: 0in; margin-top: 0in; margin-bottom: .0001pt"> > </pre> > <pre style="font-size: 10.0pt; font-family: Courier New; margin-left: > 0in; margin-right: 0in; margin-top: 0in; margin-bottom: > .0001pt"> Function/Biological Role/Expression/Localization</pre> > <pre style="font-size: 10.0pt; font-family: Courier New; margin-left: > 0in; margin-right: 0in; margin-top: 0in; margin-bottom: .0001pt"> > GO Annotations <span > style="color: red">GENE_ONTOLOGY</span></pre> > <pre style="font-size: 10.0pt; font-family: Courier New; margin-left: > 45.8pt; margin-right: 0in; margin-top: 0in; margin-bottom: > .0001pt">Gene Expression Data (Microarray, EST, SAGE, MPSS, in-situ, > etc..) <span style="color: red">(not specified)</span></pre> > <pre style="font-size: 10.0pt; font-family: Courier New; margin-left: > 0in; margin-right: 0in; margin-top: 0in; margin-bottom: .0001pt"> > (supra- cellular) Localization > (immunohistochemistry, GFP/YFP)</pre> > <pre style="font-size: 10.0pt; font-family: Courier New; margin-left: > 0in; margin-right: 0in; margin-top: 0in; margin-bottom: > .0001pt"> </pre> > <pre style="font-size: 10.0pt; font-family: Courier New; margin-left: > 0in; margin-right: 0in; margin-top: 0in; margin-bottom: > .0001pt"> </pre> > <pre style="font-size: 10.0pt; font-family: Courier New; margin-left: > 0in; margin-right: 0in; margin-top: 0in; margin-bottom: > .0001pt">Alleles and Phenotypes <span style="color: > red">FUNCTION</span></pre> > <pre style="font-size: 10.0pt; font-family: Courier New; margin-left: > 0in; margin-right: 0in; margin-top: 0in; margin-bottom: .0001pt"> > Sequence Variation (nt sequence > [C->A at 2344 bp] and coding</pre> > <pre style="font-size: 10.0pt; font-family: Courier New; margin-left: > 0in; margin-right: 0in; margin-top: 0in; margin-bottom: .0001pt"> > sequence change[ e.g.nonsense mutation at AA 467]) <span style="color: > red">(not specified)</span></pre> > <pre style="font-size: 10.0pt; font-family: Courier New; margin-left: > 0in; margin-right: 0in; margin-top: 0in; margin-bottom: .0001pt"> > Variation Type:(e.g. insertion, > deletion, etc..) <span style="color: red">(not specified)</span></pre> > <pre style="font-size: 10.0pt; font-family: Courier New; margin-left: > 0in; margin-right: 0in; margin-top: 0in; margin-bottom: .0001pt"> > Mutagen: e.g. EMS, RNAi et... > <span style="color: red">(not specified)</span></pre> > <pre style="font-size: 10.0pt; font-family: Courier New; margin-left: > 0in; margin-right: 0in; margin-top: 0in; margin-bottom: .0001pt"> > Type: e.g. hypermorph, > neomorph,etc.. <span style="color: red">(not specified)</span></pre> > <pre style="font-size: 10.0pt; font-family: Courier New; margin-left: > 0in; margin-right: 0in; margin-top: 0in; margin-bottom: .0001pt"> > Phenotype <span style="color: > red">FUNCTION (Phenotype)</span></pre> > <pre style="font-size: 10.0pt; font-family: Courier New; margin-left: > 0in; margin-right: 0in; margin-top: 0in; margin-bottom: .0001pt"> > </pre> > <pre style="font-size: 10.0pt; font-family: Courier New; margin-left: > 0in; margin-right: 0in; margin-top: 0in; margin-bottom: > .0001pt"> Pathways and Interactions <span style="color: > red">FUNCTION</span></pre> > <pre style="font-size: 10.0pt; font-family: Courier New; margin-left: > 0in; margin-right: 0in; margin-top: 0in; margin-bottom: .0001pt"> > Genetic Pathways <span > style="color: red">(not specified)</span></pre> > <pre style="font-size: 10.0pt; font-family: Courier New; margin-left: > 0in; margin-right: 0in; margin-top: 0in; margin-bottom: .0001pt"> > Metabolic Pathways <span > style="color: red">(not specified)</span></pre> > <pre style="font-size: 10.0pt; font-family: Courier New; margin-left: > 0in; margin-right: 0in; margin-top: 0in; margin-bottom: .0001pt"> > Signaling Pathways <span > style="color: red">(not specified)</span></pre> > <pre style="font-size: 10.0pt; font-family: Courier New; margin-left: > 0in; margin-right: 0in; margin-top: 0in; margin-bottom: .0001pt"> > Interacting Partners (binds to > DNA/binds to Protein/modifies X)</pre> > <pre style="font-size: 10.0pt; font-family: Courier New; margin-left: > 0in; margin-right: 0in; margin-top: 0in; margin-bottom: > .0001pt"> <span > style="color: red">FUNCTION (Interactions)</span></pre> > <pre style="font-size: 10.0pt; font-family: Courier New; margin-left: > 0in; margin-right: 0in; margin-top: 0in; margin-bottom: > .0001pt"> </pre> > <pre style="font-size: 10.0pt; font-family: Courier New; margin-left: > 0in; margin-right: 0in; margin-top: 0in; margin-bottom: .0001pt"> > Protein * </pre> > <pre style="font-size: 10.0pt; font-family: Courier New; margin-left: > 0in; margin-right: 0in; margin-top: 0in; margin-bottom: > .0001pt"> Sequence*</pre> > <pre style="font-size: 10.0pt; font-family: Courier New; margin-left: > 0in; margin-right: 0in; margin-top: 0in; margin-bottom: .0001pt"> > Domains/Motifs* <span > style="color: red">FUNCTION (Protein_domains)</span></pre> > <pre style="font-size: 10.0pt; font-family: Courier New; margin-left: > 0in; margin-right: 0in; margin-top: 0in; margin-bottom: .0001pt"> > Post-translational modifications > <span style="color: red">(not specified)</span></pre> > <pre style="font-size: 10.0pt; font-family: Courier New; margin-left: > 0in; margin-right: 0in; margin-top: 0in; margin-bottom: .0001pt"> > Tryptic Digest Patterns <span > style="color: red">(not specified)</span></pre> > <pre style="font-size: 10.0pt; font-family: Courier New; margin-left: > 0in; margin-right: 0in; margin-top: 0in; margin-bottom: .0001pt"> > pI* <span style="color: red">(not > specified)</span></pre> > <pre style="font-size: 10.0pt; font-family: Courier New; margin-left: > 0in; margin-right: 0in; margin-top: 0in; margin-bottom: .0001pt"> > Molecular Weight* <span > style="color: red">(not specified)</span></pre> > <pre style="font-size: 10.0pt; font-family: Courier New; margin-left: > 0in; margin-right: 0in; margin-top: 0in; margin-bottom: .0001pt"> > Homologies* <span style="color: > red">(SIMILAR_GENES)</span></pre> > <pre style="font-size: 10.0pt; font-family: Courier New; margin-left: > 0in; margin-right: 0in; margin-top: 0in; margin-bottom: .0001pt"> > </pre> > <pre style="font-size: 10.0pt; font-family: Courier New; margin-left: > 0in; margin-right: 0in; margin-top: 0in; margin-bottom: > .0001pt"> Reagents <span style="color: red">REAGENTS > </span></pre> > <pre style="font-size: 10.0pt; font-family: Courier New; margin-left: > 0in; margin-right: 0in; margin-top: 0in; margin-bottom: > .0001pt"> Clones <span > style="color: red">(not specified)</span></pre> > <pre style="font-size: 10.0pt; font-family: Courier New; margin-left: > 0in; margin-right: 0in; margin-top: 0in; margin-bottom: .0001pt"> > Antibodies <span style="color: > red">(not specified)</span></pre> > <pre style="font-size: 10.0pt; font-family: Courier New; margin-left: > 0in; margin-right: 0in; margin-top: 0in; margin-bottom: .0001pt"> > Strains (e.g. seed stocks) <span > style="color: red">(not specified)</span></pre> > <pre style="font-size: 10.0pt; font-family: Courier New; margin-left: > 0in; margin-right: 0in; margin-top: 0in; margin-bottom: .0001pt"> > </pre> > <pre style="font-size: 10.0pt; font-family: Courier New; margin-left: > 0in; margin-right: 0in; margin-top: 0in; margin-bottom: > .0001pt"> Literature <span style="color: > red">LITERATURE</span></pre> > <h2>Rat Genome Database</h2> > <pre style="font-size: 10.0pt; font-family: Courier New; margin-left: > 0in; margin-right: 0in; margin-top: 0in; margin-bottom: > .0001pt">DATABASE ID <span style="color: red">BASIC_INFORMATION > (GeneID)</span></pre> > <pre style="font-size: 10.0pt; font-family: Courier New; margin-left: > 0in; margin-right: 0in; margin-top: 0in; margin-bottom: .0001pt"> > SYMBOL & NAME <span style="color: red">BASIC_INFORMATION > (Symbol|Full_name)</span></pre> > <pre style="font-size: 10.0pt; font-family: Courier New; margin-left: > 0in; margin-right: 0in; margin-top: 0in; margin-bottom: .0001pt"> > ALIAS_SYMBOL & NAME <span style="color: red">BASIC_INFORMATION > (Synonyms)</span></pre> > <pre style="font-size: 10.0pt; font-family: Courier New; margin-left: > 0in; margin-right: 0in; margin-top: 0in; margin-bottom: .0001pt"> > DESCRIPTION - brief (~250 char) text; basic info, including > function,</pre> > <pre style="font-size: 10.0pt; font-family: Courier New; margin-left: > 0in; margin-right: 0in; margin-top: 0in; margin-bottom: .0001pt"> > process, disease, etc.; why someone would be interested in the gene > </pre> > <pre style="font-size: 10.0pt; font-family: Courier New; margin-left: > 0in; margin-right: 0in; margin-top: 0in; margin-bottom: > .0001pt"> SEQUENCE ACC IDs with links <span style="color: > red">SUMMARY</span></pre> > <pre style="font-size: 10.0pt; font-family: Courier New; margin-left: > 0in; margin-right: 0in; margin-top: 0in; margin-bottom: .0001pt"> > GenBank/EMBL/DDBJ</pre> > <pre style="font-size: 10.0pt; font-family: Courier New; margin-left: > 0in; margin-right: 0in; margin-top: 0in; margin-bottom: .0001pt"> > > mRNA</pre> > <pre style="font-size: 10.0pt; font-family: Courier New; margin-left: > 0in; margin-right: 0in; margin-top: 0in; margin-bottom: .0001pt"> > > protein</pre> > <pre style="font-size: 10.0pt; font-family: Courier New; margin-left: > 0in; margin-right: 0in; margin-top: 0in; margin-bottom: .0001pt"> > > genomic</pre> > <pre style="font-size: 10.0pt; font-family: Courier New; margin-left: > 0in; margin-right: 0in; margin-top: 0in; margin-bottom: .0001pt"> > > contig</pre> > <pre style="font-size: 10.0pt; font-family: Courier New; margin-left: > 0in; margin-right: 0in; margin-top: 0in; margin-bottom: .0001pt"> > > unigene</pre> > <pre style="font-size: 10.0pt; font-family: Courier New; margin-left: > 0in; margin-right: 0in; margin-top: 0in; margin-bottom: .0001pt"> > Refseq (mRNA and protein)</pre> > <pre style="font-size: 10.0pt; font-family: Courier New; margin-left: > 0in; margin-right: 0in; margin-top: 0in; margin-bottom: .0001pt"> > Primers</pre> > <pre style="font-size: 10.0pt; font-family: Courier New; margin-left: > 0in; margin-right: 0in; margin-top: 0in; margin-bottom: > .0001pt"> </pre> > <pre style="font-size: 10.0pt; font-family: Courier New; margin-left: > 0in; margin-right: 0in; margin-top: 0in; margin-bottom: .0001pt"> > REFERENCES <span style="color: red">LITERATURE > (Reference)</span></pre> > <pre style="font-size: 10.0pt; font-family: Courier New; margin-left: > 0in; margin-right: 0in; margin-top: 0in; margin-bottom: .0001pt"> > Curated - database ID and other > IDs, e.g., PubMed </pre> > <pre style="font-size: 10.0pt; font-family: Courier New; margin-left: > 0in; margin-right: 0in; margin-top: 0in; margin-bottom: > .0001pt"> Others > </pre> > <pre style="font-size: 10.0pt; font-family: Courier New; margin-left: > 0in; margin-right: 0in; margin-top: 0in; margin-bottom: > .0001pt"> </pre> > <pre style="font-size: 10.0pt; font-family: Courier New; margin-left: > 0in; margin-right: 0in; margin-top: 0in; margin-bottom: .0001pt"> > EXTERNA.L DATABASE IDs and LINKS <span style="color: red">FUNCTION > (External_links)</span></pre> > <pre style="font-size: 10.0pt; font-family: Courier New; margin-left: > 0in; margin-right: 0in; margin-top: 0in; margin-bottom: .0001pt"> > Uniprot</pre> > <pre style="font-size: 10.0pt; font-family: Courier New; margin-left: > 0in; margin-right: 0in; margin-top: 0in; margin-bottom: .0001pt"> > Ensembl</pre> > <pre style="font-size: 10.0pt; font-family: Courier New; margin-left: > 0in; margin-right: 0in; margin-top: 0in; margin-bottom: .0001pt"> > Entrez gene</pre> > <pre style="font-size: 10.0pt; font-family: Courier New; margin-left: > 0in; margin-right: 0in; margin-top: 0in; margin-bottom: .0001pt"> > OMIM</pre> > <pre style="font-size: 10.0pt; font-family: Courier New; margin-left: > 0in; margin-right: 0in; margin-top: 0in; margin-bottom: .0001pt"> > Kegg</pre> > <pre style="font-size: 10.0pt; font-family: Courier New; margin-left: > 0in; margin-right: 0in; margin-top: 0in; margin-bottom: .0001pt"> > Reactome</pre> > <pre style="font-size: 10.0pt; font-family: Courier New; margin-left: > 0in; margin-right: 0in; margin-top: 0in; margin-bottom: .0001pt"> > BIND</pre> > <pre style="font-size: 10.0pt; font-family: Courier New; margin-left: > 0in; margin-right: 0in; margin-top: 0in; margin-bottom: .0001pt"> > etc.</pre> > <pre style="font-size: 10.0pt; font-family: Courier New; margin-left: > 0in; margin-right: 0in; margin-top: 0in; margin-bottom: > .0001pt"> </pre> > <pre style="font-size: 10.0pt; font-family: Courier New; margin-left: > 0in; margin-right: 0in; margin-top: 0in; margin-bottom: .0001pt"> > MAPPING DATA <span style="color: red">LOCATION</span></pre> > <pre style="font-size: 10.0pt; font-family: Courier New; margin-left: > 0in; margin-right: 0in; margin-top: 0in; margin-bottom: .0001pt"> > Chromosome <span style="color: > red">LOCATION (Chromosome)</span></pre> > <pre style="font-size: 10.0pt; font-family: Courier New; margin-left: > 0in; margin-right: 0in; margin-top: 0in; margin-bottom: .0001pt"> > Band </pre> > <pre style="font-size: 10.0pt; font-family: Courier New; margin-left: > 0in; margin-right: 0in; margin-top: 0in; margin-bottom: > .0001pt"> Position on > specific maps (genetic, RH) <span style="color: red">LOCATION > (map)</span></pre> > <pre style="font-size: 10.0pt; font-family: Courier New; margin-left: > 0in; margin-right: 0in; margin-top: 0in; margin-bottom: .0001pt"> > Genomic position - start and stop > plus build</pre> > <pre style="font-size: 10.0pt; font-family: Courier New; margin-left: > .5in; margin-right: 0in; margin-top: 0in; margin-bottom: .0001pt"> > Links to images such as browser images (we actually show the </pre> > <pre style="font-size: 10.0pt; font-family: Courier New; margin-left: > .5in; margin-right: 0in; margin-top: 0in; margin-bottom: > .0001pt"> browser image in addition to links.) <span > style="color: red">LOCATION (Genome_map)</span></pre> > <pre style="font-size: 10.0pt; font-family: Courier New; margin-left: > 0in; margin-right: 0in; margin-top: 0in; margin-bottom: .0001pt"> > </pre> > <pre style="font-size: 10.0pt; font-family: Courier New; margin-left: > 0in; margin-right: 0in; margin-top: 0in; margin-bottom: > .0001pt">RELATED GENES <span style="color: > red">SIMILAR_GENES</span></pre> > <pre style="font-size: 10.0pt; font-family: Courier New; margin-left: > 45.8pt; margin-right: 0in; margin-top: 0in; margin-bottom: > .0001pt">Splice variants <span style="color: red">SIMILAR_GENES > (Similarity) (Description)</span></pre> > <pre style="font-size: 10.0pt; font-family: Courier New; margin-left: > 45.8pt; margin-right: 0in; margin-top: 0in; margin-bottom: > .0001pt">Pseudogenes <span style="color: red">SIMILAR_GENES > (Similarity) (Description)</span></pre> > <pre style="font-size: 10.0pt; font-family: Courier New; margin-left: > 45.8pt; margin-right: 0in; margin-top: 0in; margin-bottom: > .0001pt">Alleles <span style="color: red">SIMILAR_GENES (Similarity) > (Description)</span></pre> > <pre style="font-size: 10.0pt; font-family: Courier New; margin-left: > 0in; margin-right: 0in; margin-top: 0in; margin-bottom: .0001pt"> > etc.</pre> > <pre style="font-size: 10.0pt; font-family: Courier New; margin-left: > 0in; margin-right: 0in; margin-top: 0in; margin-bottom: .0001pt"> > OTHER DB OBJECTS ASSOC. WITH THE GENE </pre> > <pre style="font-size: 10.0pt; font-family: Courier New; margin-left: > 0in; margin-right: 0in; margin-top: 0in; margin-bottom: > .0001pt"> Strains</pre> > <pre style="font-size: 10.0pt; font-family: Courier New; margin-left: > 0in; margin-right: 0in; margin-top: 0in; margin-bottom: .0001pt"> > QTL</pre> > <pre style="font-size: 10.0pt; font-family: Courier New; margin-left: > 0in; margin-right: 0in; margin-top: 0in; margin-bottom: .0001pt"> > ESTs</pre> > <pre style="font-size: 10.0pt; font-family: Courier New; margin-left: > 0in; margin-right: 0in; margin-top: 0in; margin-bottom: .0001pt"> > SSLP</pre> > <pre style="font-size: 10.0pt; font-family: Courier New; margin-left: > 0in; margin-right: 0in; margin-top: 0in; margin-bottom: .0001pt"> > etc.</pre> > <pre style="font-size: 10.0pt; font-family: Courier New; margin-left: > 0in; margin-right: 0in; margin-top: 0in; margin-bottom: > .0001pt"> </pre> > <pre style="font-size: 10.0pt; font-family: Courier New; margin-left: > 0in; margin-right: 0in; margin-top: 0in; margin-bottom: .0001pt"> > HOMOLOGS <span style="color: red">SIMILAR_GENES</span></pre> > <pre style="font-size: 10.0pt; font-family: Courier New; margin-left: > 0in; margin-right: 0in; margin-top: 0in; margin-bottom: > .0001pt"> </pre> > <pre style="font-size: 10.0pt; font-family: Courier New; margin-left: > 0in; margin-right: 0in; margin-top: 0in; margin-bottom: .0001pt"> GENE > TYPE <span style="color: red">GENE_PRODUCT (Gene_type)</span></pre> > <pre style="font-size: 10.0pt; font-family: Courier New; margin-left: > 0in; margin-right: 0in; margin-top: 0in; margin-bottom: .0001pt"> > Splice variant </pre> > <pre style="font-size: 10.0pt; font-family: Courier New; margin-left: > 0in; margin-right: 0in; margin-top: 0in; margin-bottom: > .0001pt"> Pseudogene > </pre> > <pre style="font-size: 10.0pt; font-family: Courier New; margin-left: > 0in; margin-right: 0in; margin-top: 0in; margin-bottom: > .0001pt"> Alleles </pre> > <pre style="font-size: 10.0pt; font-family: Courier New; margin-left: > 0in; margin-right: 0in; margin-top: 0in; margin-bottom: > .0001pt"> </pre> > <pre style="font-size: 10.0pt; font-family: Courier New; margin-left: > 0in; margin-right: 0in; margin-top: 0in; margin-bottom: > .0001pt"> </pre> > <pre style="font-size: 10.0pt; font-family: Courier New; margin-left: > 0in; margin-right: 0in; margin-top: 0in; margin-bottom: .0001pt"> GENE > EVIDENCE </pre> > <pre style="font-size: 10.0pt; font-family: Courier New; margin-left: > 0in; margin-right: 0in; margin-top: 0in; margin-bottom: > .0001pt"> Known </pre> > <pre style="font-size: 10.0pt; font-family: Courier New; margin-left: > 0in; margin-right: 0in; margin-top: 0in; margin-bottom: > .0001pt"> Predicted by > homology</pre> > <pre style="font-size: 10.0pt; font-family: Courier New; margin-left: > 0in; margin-right: 0in; margin-top: 0in; margin-bottom: .0001pt"> > Predicted by EST evidence</pre> > <pre style="font-size: 10.0pt; font-family: Courier New; margin-left: > 0in; margin-right: 0in; margin-top: 0in; margin-bottom: .0001pt"> > etc.</pre> > <pre style="font-size: 10.0pt; font-family: Courier New; margin-left: > 0in; margin-right: 0in; margin-top: 0in; margin-bottom: > .0001pt"> </pre> > <pre style="font-size: 10.0pt; font-family: Courier New; margin-left: > 0in; margin-right: 0in; margin-top: 0in; margin-bottom: .0001pt"> > BIOLOGICAL DATA (CONTROLLED VOCAB/ONTOLOGIES/TEXT) <span style="color: > red">GENE_ONTOLOGY</span> </pre> > <pre style="font-size: 10.0pt; font-family: Courier New; margin-left: > 0in; margin-right: 0in; margin-top: 0in; margin-bottom: > .0001pt"> Biological Process <span style="color: > red">GENE_ONTOLOGY (Biological_process)</span></pre> > <pre style="font-size: 10.0pt; font-family: Courier New; margin-left: > 0in; margin-right: 0in; margin-top: 0in; margin-bottom: .0001pt"> > Cellular Component <span style="color: red">GENE_ONTOLOGY > (Cellular_component)</span></pre> > <pre style="font-size: 10.0pt; font-family: Courier New; margin-left: > 0in; margin-right: 0in; margin-top: 0in; margin-bottom: .0001pt"> > Disease </pre> > <pre style="font-size: 10.0pt; font-family: Courier New; margin-left: > 0in; margin-right: 0in; margin-top: 0in; margin-bottom: > .0001pt"> Domains <span style="color: red">FUNCTION > (Protein_domains)</span></pre> > <pre style="font-size: 10.0pt; font-family: Courier New; margin-left: > 0in; margin-right: 0in; margin-top: 0in; margin-bottom: .0001pt"> > Drugs effects</pre> > <pre style="font-size: 10.0pt; font-family: Courier New; margin-left: > 0in; margin-right: 0in; margin-top: 0in; margin-bottom: .0001pt"> EC > number</pre> > <pre style="font-size: 10.0pt; font-family: Courier New; margin-left: > 0in; margin-right: 0in; margin-top: 0in; margin-bottom: .0001pt"> > Evolution</pre> > <pre style="font-size: 10.0pt; font-family: Courier New; margin-left: > 0in; margin-right: 0in; margin-top: 0in; margin-bottom: .0001pt"> > Expression <span style="color: red">FUNCTION (Expression)</span></pre> > <pre style="font-size: 10.0pt; font-family: Courier New; margin-left: > 0in; margin-right: 0in; margin-top: 0in; margin-bottom: .0001pt"> > Family </pre> > <pre style="font-size: 10.0pt; font-family: Courier New; margin-left: > 0in; margin-right: 0in; margin-top: 0in; margin-bottom: > .0001pt"> Homology details <span style="color: > red">SIMILAR_GENES</span></pre> > <pre style="font-size: 10.0pt; font-family: Courier New; margin-left: > 0in; margin-right: 0in; margin-top: 0in; margin-bottom: .0001pt"> > Molecular Function <span style="color: red">FUNCTION</span></pre> > <pre style="font-size: 10.0pt; font-family: Courier New; margin-left: > 0in; margin-right: 0in; margin-top: 0in; margin-bottom: .0001pt"><span > style="color: red"> </span>Mutation/over- and underexpression</pre> > <pre style="font-size: 10.0pt; font-family: Courier New; margin-left: > 0in; margin-right: 0in; margin-top: 0in; margin-bottom: .0001pt"> > Pathway</pre> > <pre style="font-size: 10.0pt; font-family: Courier New; margin-left: > 0in; margin-right: 0in; margin-top: 0in; margin-bottom: .0001pt"> > Phenotype <span style="color: red">FUNCTION (Phenotype)</span></pre> > <pre style="font-size: 10.0pt; font-family: Courier New; margin-left: > 0in; margin-right: 0in; margin-top: 0in; margin-bottom: .0001pt"> > Physical interaction <span style="color: red">FUNCTION > (Phenotype)</span></pre> > <pre style="font-size: 10.0pt; font-family: Courier New; margin-left: > 0in; margin-right: 0in; margin-top: 0in; margin-bottom: .0001pt"> > Protein modifications</pre> > <pre style="font-size: 10.0pt; font-family: Courier New; margin-left: > 0in; margin-right: 0in; margin-top: 0in; margin-bottom: .0001pt"> > Regulation</pre> > <pre style="font-size: 10.0pt; font-family: Courier New; margin-left: > 0in; margin-right: 0in; margin-top: 0in; margin-bottom: .0001pt"> > Size</pre> > <pre style="font-size: 10.0pt; font-family: Courier New; margin-left: > 0in; margin-right: 0in; margin-top: 0in; margin-bottom: .0001pt"> > Transcript structure</pre> > <pre style="font-size: 10.0pt; font-family: Courier New; margin-left: > 0in; margin-right: 0in; margin-top: 0in; margin-bottom: .0001pt"> > etc</pre> > <b><i><span style="font-size: 14.0pt; font-family: Arial"> > <br clear="all" style="page-break-before: always"> > </span></i></b><h2>SGD Saccharomyces Genome Database</h2> > <p class="MsoNormal"> </p> > <pre style="font-size: 10.0pt; font-family: Courier New; margin-left: > 0in; margin-right: 0in; margin-top: 0in; margin-bottom: > .0001pt"> basic information <span style="color: > red">BASIC_INFORMATION</span></pre> > <pre style="font-size: 10.0pt; font-family: Courier New; margin-left: > 0in; margin-right: 0in; margin-top: 0in; margin-bottom: > .0001pt"> standard gene name > <span style="color: red">BASIC_INFORMATION (Full_name)</span></pre> > <pre style="font-size: 10.0pt; font-family: Courier New; margin-left: > 0in; margin-right: 0in; margin-top: 0in; margin-bottom: > .0001pt"> systematic locus name > <span style="color: red">BASIC_INFORMATION</span></pre> > <pre style="font-size: 10.0pt; font-family: Courier New; margin-left: > 0in; margin-right: 0in; margin-top: 0in; margin-bottom: > .0001pt"> alias <span > style="color: red">BASIC_INFORMATION (Synonyms)</span></pre> > <pre style="font-size: 10.0pt; font-family: Courier New; margin-left: > 0in; margin-right: 0in; margin-top: 0in; margin-bottom: > .0001pt"> feature type </pre> > <pre style="font-size: 10.0pt; font-family: Courier New; margin-left: > 0in; margin-right: 0in; margin-top: 0in; margin-bottom: > .0001pt"> locus > description</pre> > <pre style="font-size: 10.0pt; font-family: Courier New; margin-left: > 0in; margin-right: 0in; margin-top: 0in; margin-bottom: > .0001pt"> GO annotations <span > style="color: red">GENE_ONTOLOGY</span></pre> > <pre style="font-size: 10.0pt; font-family: Courier New; margin-left: > 0in; margin-right: 0in; margin-top: 0in; margin-bottom: > .0001pt"> > > molecular function <span style="color: red">GENE_ONTOLOGY > (Molecular_function)</span></pre> > <pre style="font-size: 10.0pt; font-family: Courier New; margin-left: > 0in; margin-right: 0in; margin-top: 0in; margin-bottom: > .0001pt"> > > biological process <span style="color: red">GENE_ONTOLOGY > (Biological_process)</span></pre> > <pre style="font-size: 10.0pt; font-family: Courier New; margin-left: > 0in; margin-right: 0in; margin-top: 0in; margin-bottom: > .0001pt"> > > cellular component <span style="color: red">GENE_ONTOLOGY > (Cellular_component)</span></pre> > <pre style="font-size: 10.0pt; font-family: Courier New; margin-left: > 0in; margin-right: 0in; margin-top: 0in; margin-bottom: > .0001pt"> > > evidence codes and references <span style="color: > red">GENE_ONTOLOGY (goevidence </span></pre> > <pre style="font-size: 10.0pt; font-family: Courier New; margin-left: > 0in; margin-right: 0in; margin-top: 0in; margin-bottom: .0001pt"><span > style="color: > red"> > > > > > | goterm)</span></pre> > <pre style="font-size: 10.0pt; font-family: Courier New; margin-left: > 0in; margin-right: 0in; margin-top: 0in; margin-bottom: > .0001pt"> pathways</pre> > <pre style="font-size: 10.0pt; font-family: Courier New; margin-left: > 0in; margin-right: 0in; margin-top: 0in; margin-bottom: > .0001pt"> gene name > description</pre> > <pre style="font-size: 10.0pt; font-family: Courier New; margin-left: > 0in; margin-right: 0in; margin-top: 0in; margin-bottom: > .0001pt"> gene product <span > style="color: red">GENE_PRODUCT</span> </pre> > <pre style="font-size: 10.0pt; font-family: Courier New; margin-left: > 0in; margin-right: 0in; margin-top: 0in; margin-bottom: > .0001pt"> mutant phenotypes > <span style="color: red">FUNCTION (Phenotypes)</span></pre> > <pre style="font-size: 10.0pt; font-family: Courier New; margin-left: > 0in; margin-right: 0in; margin-top: 0in; margin-bottom: > .0001pt"> > > phenotype type </pre> > <pre style="font-size: 10.0pt; font-family: Courier New; margin-left: > 0in; margin-right: 0in; margin-top: 0in; margin-bottom: > .0001pt"> > phenotype</pre> > <pre style="font-size: 10.0pt; font-family: Courier New; margin-left: > 0in; margin-right: 0in; margin-top: 0in; margin-bottom: > .0001pt"> > > details and references</pre> > <pre style="font-size: 10.0pt; font-family: Courier New; margin-left: > 0in; margin-right: 0in; margin-top: 0in; margin-bottom: > .0001pt"> sequence information > <span style="color: red">LOCATION</span></pre> > <pre style="font-size: 10.0pt; font-family: Courier New; margin-left: > 0in; margin-right: 0in; margin-top: 0in; margin-bottom: > .0001pt"> > > mapping info <span style="color: red">LOCATION > (Genome_map)</span></pre> > <pre style="font-size: 10.0pt; font-family: Courier New; margin-left: > 0in; margin-right: 0in; margin-top: 0in; margin-bottom: > .0001pt"> > > last update dates (coordinates and sequence)</pre> > <pre style="font-size: 10.0pt; font-family: Courier New; margin-left: > 0in; margin-right: 0in; margin-top: 0in; margin-bottom: > .0001pt"> > > subfeature details</pre> > <pre style="font-size: 10.0pt; font-family: Courier New; margin-left: > 0in; margin-right: 0in; margin-top: 0in; margin-bottom: > .0001pt"> > > subfeature > type</pre> > <pre style="font-size: 10.0pt; font-family: Courier New; margin-left: > 0in; margin-right: 0in; margin-top: 0in; margin-bottom: > .0001pt"> > > relative > coordinates</pre> > <pre style="font-size: 10.0pt; font-family: Courier New; margin-left: > 0in; margin-right: 0in; margin-top: 0in; margin-bottom: > .0001pt"> > > chromosomal > coordinates <span style="color: red">LOCATION > (Chromosome)</span></pre> > <pre style="font-size: 10.0pt; font-family: Courier New; margin-left: > 0in; margin-right: 0in; margin-top: 0in; margin-bottom: > .0001pt"> external links <span > style="color: red">FUNCTION (External_links)</span></pre> > <pre style="font-size: 10.0pt; font-family: Courier New; margin-left: > 0in; margin-right: 0in; margin-top: 0in; margin-bottom: > .0001pt"> > > Entrez</pre> > <pre style="font-size: 10.0pt; font-family: Courier New; margin-left: > 0in; margin-right: 0in; margin-top: 0in; margin-bottom: > .0001pt"> > > E.C.</pre> > <pre style="font-size: 10.0pt; font-family: Courier New; margin-left: > 0in; margin-right: 0in; margin-top: 0in; margin-bottom: > .0001pt"> > > MIPS</pre> > <pre style="font-size: 10.0pt; font-family: Courier New; margin-left: > 0in; margin-right: 0in; margin-top: 0in; margin-bottom: > .0001pt"> > > SwissProt</pre> > <pre style="font-size: 10.0pt; font-family: Courier New; margin-left: > 0in; margin-right: 0in; margin-top: 0in; margin-bottom: > .0001pt"> dbxref_id</pre> > <pre style="font-size: 10.0pt; font-family: Courier New; margin-left: > 0in; margin-right: 0in; margin-top: 0in; margin-bottom: > .0001pt"> resources</pre> > <pre style="font-size: 10.0pt; font-family: Courier New; margin-left: > 0in; margin-right: 0in; margin-top: 0in; margin-bottom: > .0001pt"> literature <span > style="color: red">LITERATURE</span></pre> > <pre style="font-size: 10.0pt; font-family: Courier New; margin-left: > 0in; margin-right: 0in; margin-top: 0in; margin-bottom: > .0001pt"> retrieve > sequences</pre> > <pre style="font-size: 10.0pt; font-family: Courier New; margin-left: > 0in; margin-right: 0in; margin-top: 0in; margin-bottom: > .0001pt"> sequence analysis > tools</pre> > <pre style="font-size: 10.0pt; font-family: Courier New; margin-left: > 0in; margin-right: 0in; margin-top: 0in; margin-bottom: > .0001pt"> protein info and > structure</pre> > <pre style="font-size: 10.0pt; font-family: Courier New; margin-left: > 0in; margin-right: 0in; margin-top: 0in; margin-bottom: > .0001pt"> protein localization > resources</pre> > <pre style="font-size: 10.0pt; font-family: Courier New; margin-left: > 0in; margin-right: 0in; margin-top: 0in; margin-bottom: > .0001pt"> external protein > interaction db"s <span style="color: red">FUNCTION > (External_links)</span></pre> > <pre style="font-size: 10.0pt; font-family: Courier New; margin-left: > 0in; margin-right: 0in; margin-top: 0in; margin-bottom: > .0001pt"> external phenotype > db"s <span style="color: red">FUNCTION > (External_links)</span></pre> > <pre style="font-size: 10.0pt; font-family: Courier New; margin-left: > 0in; margin-right: 0in; margin-top: 0in; margin-bottom: > .0001pt"> maps and displays <span > style="color: red">LOCATION (Maps)</span></pre> > <pre style="font-size: 10.0pt; font-family: Courier New; margin-left: > 0in; margin-right: 0in; margin-top: 0in; margin-bottom: > .0001pt"> sequence comparison > resources</pre> > <pre style="font-size: 10.0pt; font-family: Courier New; margin-left: > 0in; margin-right: 0in; margin-top: 0in; margin-bottom: > .0001pt"> functional > analysis</pre> > <pre style="font-size: 10.0pt; font-family: Courier New; margin-left: > 0in; margin-right: 0in; margin-top: 0in; margin-bottom: > .0001pt"> additional information <span style="color: > red">ADDITIONAL_INFORMATION</span></pre> > <pre style="font-size: 10.0pt; font-family: Courier New; margin-left: > 0in; margin-right: 0in; margin-top: 0in; margin-bottom: > .0001pt"> locus history</pre> > <pre style="font-size: 10.0pt; font-family: Courier New; margin-left: > 0in; margin-right: 0in; margin-top: 0in; margin-bottom: > .0001pt"> expression > datasets</pre> > <pre style="font-size: 10.0pt; font-family: Courier New; margin-left: > 0in; margin-right: 0in; margin-top: 0in; margin-bottom: > .0001pt"> associated > researchers</pre> > <pre style="font-size: 10.0pt; font-family: Courier New; margin-left: > 0in; margin-right: 0in; margin-top: 0in; margin-bottom: > .0001pt"> community annotation</pre> > <pre style="font-size: 10.0pt; font-family: Courier New; margin-left: > 0in; margin-right: 0in; margin-top: 0in; margin-bottom: > .0001pt"> DNA and RNA > details</pre> > <pre style="font-size: 10.0pt; font-family: Courier New; margin-left: > 0in; margin-right: 0in; margin-top: 0in; margin-bottom: > .0001pt"> protein details</pre> > <pre style="font-size: 10.0pt; font-family: Courier New; margin-left: > 0in; margin-right: 0in; margin-top: 0in; margin-bottom: > .0001pt"> interactions <span > style="color: red">FUNCTION (Interactions)</span></pre> > <pre style="font-size: 10.0pt; font-family: Courier New; margin-left: > 0in; margin-right: 0in; margin-top: 0in; margin-bottom: > .0001pt"> techniques and reagents > <span style="color: red">REAGENTS</span></pre> > <pre style="font-size: 10.0pt; font-family: Courier New; margin-left: > 0in; margin-right: 0in; margin-top: 0in; margin-bottom: > .0001pt"> alleles, strains, and > phenotypes</pre> > <p class="MsoNormal"> </p> > > </body> > > </html> |