<?xml version="1.0" encoding="ASCII"?>
<biogps><data><item><item key="rating_data"><item key="avg_stars">8</item><item key="total">1</item><item key="avg">4</item></item><item key="options"><item key="allowedSpecies"><item>human</item></item></item><item key="popularity">9.0</item><item key="description">"H-Invitational Database (H-InvDB) is an integrated database of human genes and transcripts. By extensive analyses of all human transcripts, we provide curated annotations of human genes and transcripts that include gene structures, alternative splicing isoforms, non-coding functional RNAs, protein functions, functional domains, sub-cellular localizations, metabolic pathways, protein 3D structure, genetic polymorphisms (SNPs, indels and microsatellite repeats) , relation with diseases, gene expression profiling, and molecular evolutionary features , protein-protein interactions (PPIs) and gene families/groups. This database is produced by the "Genome Information Integration Project" (2005-) based upon the annotation technology established in the H-Invitational Project for annotation of human full-length cDNAs."</item><item key="tags"><item>annotation</item><item>splicing</item><item>transcript</item></item><item key="url">http://h-invitational.jp/hinv/c-search/keyidsearch.do?KEN_TYPE=CDNA_DB-REFERENCE_ENTREZGENE&amp;KEN_STR={{EntrezGene}}</item><item key="lastmodified">2011-05-03 22:47:18</item><item key="usage_data"><item key="layouts">9.0</item><item key="users">5</item></item><item key="created">2010-02-08 22:12:55</item><item key="id">610</item><item key="shortUrl">h-invitational.jp</item><item key="role_permission"><item>biogpsusers</item></item><item key="short_description">"H-Invitational Database (H-InvDB) is an integrated database of human genes and transcripts. By extensive analyses of all human...</item><item key="in">plugin</item><item key="owner"><item key="username">cwu</item><item key="url">/profile/2/cwu</item><item key="name">Chunlei Wu</item></item><item key="permission_style">public</item><item key="type">iframe</item><item key="species"><item>human</item></item><item key="name">H-InvDB</item></item><item><item key="rating_data"><item key="avg_stars">0</item><item key="total">0</item><item key="avg">0</item></item><item key="options"><item key="allowedSpecies"><item>human</item><item>mouse</item></item></item><item key="description">FuncBase is a public database of predicted gene-function annotations for Yeast, Mouse and Human genes, overlayed upon the experimentally verified annotations as taken from the SGD, MGI and Ensembl Gene databases, respectively.

FuncBase displays three aspects of gene function predictions:
- First, for a particular gene, users can view all functions ranked by certainty that the corresponding gene-function pair is a true annotation.
- Second, for a particular function, users can view all genes ranked by certainty.
- The third aspect is functional linkage predictions, displayed alongside the first two aspects as gene-centered and function-centered images, respectively, and editable via Cytoscape. These functional linkage graphs are independently informative, though they are also used as a step in one of the gene function prediction techniques whose certainty scores are displaying on this site, so they can be treated as evidence.</item><item key="created">2010-06-02 12:28:13</item><item key="url">http://func.med.harvard.edu/human/genes/list_functional_scores/ENTREZ_GENE:{{EntrezGene}}</item><item key="lastmodified">2011-05-03 22:46:52</item><item key="usage_data"><item key="layouts">9.0</item><item key="users">7</item></item><item key="popularity">9.0</item><item key="id">711</item><item key="shortUrl">func.med.harvard.edu</item><item key="role_permission"><item>biogpsusers</item></item><item key="short_description">FuncBase is a public database of predicted gene-function annotations for Yeast, Mouse and Human genes, overlayed upon the experimentally...</item><item key="in">plugin</item><item key="owner"><item key="username">hjmollenkopf</item><item key="url">/profile/3325/hjmollenkopf</item><item key="name">Hans-Joachim Mollenkopf</item></item><item key="permission_style">public</item><item key="type">iframe</item><item key="species"><item>human</item><item>mouse</item></item><item key="name">FuncBase</item></item><item><item key="rating_data"><item key="avg_stars">0</item><item key="total">0</item><item key="avg">0</item></item><item key="options"><item key="allowedSpecies"><item>human</item><item>frog</item></item></item><item key="popularity">9.0</item><item key="description">All cancers arise as a result of the acquisition of a series of fixed DNA sequence abnormalities, mutations, many of which ultimately confer a growth advantage upon the cells in which they have occurred. There is a vast amount of information available in the published scientific literature about these changes. COSMIC is designed to store and display somatic mutation information and related details and contains information relating to human cancers.</item><item key="tags"><item>cancer</item><item>genetics</item><item>mutation</item><item>snp</item></item><item key="url">http://www.sanger.ac.uk/perl/genetics/CGP/cosmic?action=bygene&amp;ln={{Symbol}}</item><item key="lastmodified">2011-05-03 22:46:35</item><item key="usage_data"><item key="layouts">9.0</item><item key="users">7</item></item><item key="created">2010-12-15 21:46:49</item><item key="id">850</item><item key="shortUrl">www.sanger.ac.uk</item><item key="role_permission"><item>biogpsusers</item></item><item key="short_description">All cancers arise as a result of the acquisition of a series of fixed DNA sequence abnormalities, mutations, many of which ultimately...</item><item key="in">plugin</item><item key="owner"><item key="username">asu</item><item key="url">/profile/3/asu</item><item key="name">Andrew Su</item></item><item key="permission_style">public</item><item key="type">iframe</item><item key="species"><item>human</item><item>frog</item></item><item key="name">COSMIC -- Catalogue Of Somatic Mutations In Cancer (Gene View)</item></item><item><item key="rating_data"><item key="avg_stars">8</item><item key="total">1</item><item key="avg">4</item></item><item key="options">None</item><item key="popularity">9.0</item><item key="description">SciBite a free, biomedical search engine and information alerting service, focused on drug discovery. We index 1000s of papers, patents, blogs, grants, clinical trials and newsfeeds and find the articles that matter for your target, drug, disease or therapeutic area, right across the drug pipeline. The BioGPS plugin will connect any human gene to the SciBite news stream page.

We're still in beta, so we expect a number of genes will produce no results- please feed these back and we'll fix it within 24 hours :) thanks!</item><item key="tags"><item>disease</item><item>drugs</item><item>literature</item><item>news</item></item><item key="url">http://www.scibite.com/site/topic/GENE:{{Symbol}}</item><item key="lastmodified">2012-02-28 17:00:34</item><item key="usage_data"><item key="layouts">9.0</item><item key="users">8</item></item><item key="created">2012-02-28 16:57:44</item><item key="id">968</item><item key="shortUrl">www.scibite.com</item><item key="role_permission"><item>biogpsusers</item></item><item key="short_description">A live news stream related to this gene from SciBite open drug intelligence</item><item key="in">plugin</item><item key="owner"><item key="username">leeh49</item><item key="url">/profile/5472/leeh49</item><item key="name">leeh49</item></item><item key="permission_style">public</item><item key="type">iframe</item><item key="species"><item>human</item></item><item key="name">SciBite, open drug discovery intelligence</item></item><item><item key="rating_data"><item key="avg_stars">0</item><item key="total">0</item><item key="avg">0</item></item><item key="options">None</item><item key="description">Search for a variety of related products, including:

    Biomolecule
    cDNA
    Antibodies
    RNAi
    siRNA
    Inhibitor
    shRNA
    Chemicals
    RNA
    miRNA
    Tissues, Lysates &amp; Extracts
    Oligo/Primer
    Assay Kit
    Cells &amp; Strains
    DNA
    Vector
    miRNA 3&#180; UTR Targets (Human)
    miRNA 3&#180; UTR Targets (Mouse)
    miRNA 3&#180; UTR Targets (Rat)
    Other Kinase Inhibitors
</item><item key="created">2009-03-17 18:42:31</item><item key="url">http://www.biocompare.com/Search.aspx?st=r&amp;sg=0&amp;c=0&amp;so=a&amp;s={{Symbol}}</item><item key="lastmodified">2012-08-01 22:32:58</item><item key="usage_data"><item key="layouts">9.0</item><item key="users">8</item></item><item key="popularity">9.0</item><item key="id">387</item><item key="shortUrl">www.biocompare.com</item><item key="role_permission"><item>biogpsusers</item></item><item key="short_description">No summary provided.</item><item key="in">plugin</item><item key="owner"><item key="username">asu</item><item key="url">/profile/3/asu</item><item key="name">Andrew Su</item></item><item key="permission_style">public</item><item key="type">iframe</item><item key="species"><item>human</item><item>mouse</item><item>rat</item><item>fruitfly</item><item>nematode</item><item>zebrafish</item><item>thale-cress</item><item>frog</item><item>pig</item></item><item key="name">Biocompare</item></item><item><item key="rating_data"><item key="avg_stars">0</item><item key="total">0</item><item key="avg">0</item></item><item key="options"><item key="allowedSpecies"><item>human</item><item>mouse</item></item></item><item key="popularity">9.0</item><item key="description">SNPedia is a wiki investigating human genetics that shares information about the effects of variations in DNA, citing peer-reviewed scientific publications.</item><item key="tags"><item>mutation</item><item>snp</item><item>variation</item><item>wiki</item></item><item key="url">http://www.snpedia.com/index.php/Special:SearchByProperty?title=Special%3ASearchByProperty&amp;property=In+gene&amp;value={{Symbol}}</item><item key="lastmodified">2011-05-03 22:49:27</item><item key="usage_data"><item key="layouts">9.0</item><item key="users">8</item></item><item key="created">2010-09-22 00:11:16</item><item key="id">813</item><item key="shortUrl">www.snpedia.com</item><item key="role_permission"><item>biogpsusers</item></item><item key="short_description">SNPedia is a wiki investigating human genetics that shares information about the effects of variations in DNA, citing peer-reviewed...</item><item key="in">plugin</item><item key="owner"><item key="username">sbatalov</item><item key="url">/profile/89/sbatalov</item><item key="name">Serge Batalov</item></item><item key="permission_style">public</item><item key="type">iframe</item><item key="species"><item>human</item><item>mouse</item></item><item key="name">SNPedia</item></item><item><item key="rating_data"><item key="avg_stars">0</item><item key="total">0</item><item key="avg">0</item></item><item key="options"><item key="allowedSpecies"><item>human</item></item></item><item key="description"/><item key="created">2009-11-17 17:12:22</item><item key="url">http://ctd.mdibl.org/detail.go?type=gene&amp;db=GENE&amp;acc={{EntrezGene}}</item><item key="lastmodified">2011-05-03 22:46:39</item><item key="usage_data"><item key="layouts">8.0</item><item key="users">7</item></item><item key="popularity">8.0</item><item key="id">580</item><item key="shortUrl">ctd.mdibl.org</item><item key="role_permission"><item>biogpsusers</item></item><item key="short_description">No summary provided.</item><item key="in">plugin</item><item key="owner"><item key="username">asu</item><item key="url">/profile/3/asu</item><item key="name">Andrew Su</item></item><item key="permission_style">public</item><item key="type">iframe</item><item key="species"><item>human</item></item><item key="name">Comparative Toxicogenomics Database (CTD)</item></item><item><item key="rating_data"><item key="avg_stars">0</item><item key="total">0</item><item key="avg">0</item></item><item key="options">None</item><item key="popularity">8.0</item><item key="description">TreeFam (Tree families database) is a database of phylogenetic trees of animal genes. It aims at developing a curated resource that gives reliable information about ortholog and paralog assignments, and evolutionary history of various gene families.

TreeFam defines a gene family as a group of genes that evolved after the speciation of single-metazoan animals. It also tries to include outgroup genes like yeast (S. cerevisiae and S. pombe) and plant (A. thaliana) to reveal these distant members.

TreeFam is also an ortholog database. Unlike other pairwise alignment based ones, TreeFam infers orthologs by means of gene trees. It fits a gene tree into the universal species tree and finds historical duplications, speciations and losses events. TreeFam uses this information to evaluate tree building, guide manual curation, and infer complex ortholog and paralog relations.

The basic elements of TreeFam are gene families that can be divided into two parts: TreeFam-A and TreeFam-B families. TreeFam-B families are automatically created. They might contain errors given complex phylogenies. TreeFam-A families are manually curated from TreeFam-B ones. Family names and node names are assigned at the same time. The ultimate goal of TreeFam is to present a curated resource for all the families.</item><item key="tags"><item>families</item><item>ortholog</item><item>paralog</item><item>phylogenetic</item><item>tree</item></item><item key="url">http://www.treefam.org/cgi-bin/TFseq.pl?id={{EnsemblGene}}</item><item key="lastmodified">2009-05-06 21:49:09</item><item key="usage_data"><item key="layouts">8.0</item><item key="users">6</item></item><item key="created">2009-05-06 21:49:09</item><item key="id">442</item><item key="shortUrl">www.treefam.org</item><item key="role_permission"><item>biogpsusers</item></item><item key="short_description">TreeFam (Tree families database) is a database of phylogenetic trees of animal genes. It aims at developing a curated resource that gives...</item><item key="in">plugin</item><item key="owner"><item key="username">ivaagenes</item><item key="url">/profile/877/ivaagenes</item><item key="name">Ian Vaagenes</item></item><item key="permission_style">public</item><item key="type">iframe</item><item key="species"><item>human</item><item>mouse</item><item>rat</item><item>fruitfly</item><item>nematode</item><item>zebrafish</item><item>thale-cress</item><item>frog</item><item>pig</item></item><item key="name">Treefam</item></item><item><item key="rating_data"><item key="avg_stars">0</item><item key="total">0</item><item key="avg">0</item></item><item key="options"><item key="certified_owner">True</item></item><item key="description"/><item key="created">2009-09-03 21:54:06</item><item key="url">http://kb.psi-structuralgenomics.org/KB/search.do?SSIDSearch=KeywordSearch&amp;query={{Symbol}}</item><item key="lastmodified">2010-06-09 16:56:42</item><item key="usage_data"><item key="layouts">8.0</item><item key="users">7</item></item><item key="popularity">8.0</item><item key="id">512</item><item key="shortUrl">kb.psi-structuralgenomics.org</item><item key="role_permission"><item>biogpsusers</item></item><item key="short_description">No summary provided.</item><item key="in">plugin</item><item key="owner"><item key="username">kiraanthony</item><item key="url">/profile/1373/kiraanthony</item><item key="name">Kira Anthony</item></item><item key="permission_style">public</item><item key="type">iframe</item><item key="species"><item>human</item><item>mouse</item><item>rat</item><item>fruitfly</item><item>nematode</item><item>zebrafish</item><item>thale-cress</item><item>frog</item><item>pig</item></item><item key="name">PSI Structural Genomics Knowledgebase</item></item><item><item key="rating_data"><item key="avg_stars">0</item><item key="total">0</item><item key="avg">0</item></item><item key="options">None</item><item key="popularity">8.0</item><item key="description">Search by gene symbol at Google.</item><item key="tags"><item>gene</item><item>google</item><item>literature</item><item>search</item><item>symbol</item></item><item key="url">http://www.google.com/custom?q={{symbol}}</item><item key="lastmodified">2013-06-27 17:33:13</item><item key="usage_data"><item key="layouts">8.0</item><item key="users">7</item></item><item key="created">2008-06-04 18:41:15</item><item key="id">68</item><item key="shortUrl">www.google.com</item><item key="role_permission"><item>biogpsusers</item></item><item key="short_description">Search by gene symbol at Google.</item><item key="in">plugin</item><item key="owner"><item key="username">asu</item><item key="url">/profile/3/asu</item><item key="name">Andrew Su</item></item><item key="permission_style">public</item><item key="type">iframe</item><item key="species"><item>human</item><item>mouse</item><item>rat</item><item>fruitfly</item><item>nematode</item><item>zebrafish</item><item>thale-cress</item><item>frog</item><item>pig</item></item><item key="name">Google search (gene symbol)</item></item></data></biogps>
