Msigdb v2 release notes

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Release notes to be supplied.
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<br />Details on how the gene set databases were generated is provided below:<br /><br /><span style="font-weight: bold; color: rgb(255, 0, 0);">C1 (Positional gene sets)</span><br /><br />Cytogenetic locations were parsed from hugo and entrez (release x). When there were conflicts, the Entrez entry was used.<br /><br /><br /><span style="font-weight: bold; color: rgb(255, 0, 0);">C2 (Curated gene sets)</span><br /><br />C2 sets were curated from several sources including:<br /><br />
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<p style="line-height: 150%;" class="MsoNormal"><em style=""><u><span style="font-family: Arial;">Online pathway databases</span></u></em><em style=""><span style="font-family: Arial;">: </span></em><span style="font-family: Arial;">Several online resources provide catalogs of well studied metabolic and signaling pathways as well as functional categories of genes. We downloaded gene sets from 12 such databases into our system.</span></p>
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<p style="line-height: 150%;" class="MsoNormal">  </p>
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<p class="MsoNormal"><span style="font-family: Arial;"><o:p>&nbsp;</o:p></span></p>
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<table cellspacing="0" cellpadding="0" border="1" style="border: medium none ; border-collapse: collapse; width: 872px; height: 602px;" class="MsoTableGrid">
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            <p align="center" style="text-align: center;" class="MsoNormal"><strong style=""><span style="font-family: Arial;">NAME<o:p></o:p></span></strong></p>
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            <p align="center" style="text-align: center;" class="MsoNormal"><strong style=""><span style="font-family: Arial;">URL /  REFERENCE<o:p></o:p></span></strong></p>
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        <tr style="height: 13.2pt;">
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            <p class="MsoNormal"><span style="font-family: Arial;">BioCarta<o:p></o:p></span></p>
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            <p class="MsoNormal"><span style="font-family: Arial;"><a href="http://www.biocarta.com/">http://www.biocarta.com</a><o:p></o:p></span></p>
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            <p class="MsoNormal"><span style="font-family: Arial;">Signaling pathway database<o:p></o:p></span></p>
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            <p class="MsoNormal"><span style="font-family: Arial;"><a href="http://www.grt.kyushu-u.ac.jp/spad/menu.html">http://www.grt.kyushu-u.ac.jp/spad/menu.html</a><o:p></o:p></span></p>
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        <tr style="height: 14.25pt;">
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            <p class="MsoNormal"><span style="font-family: Arial;">Signaling gateway<o:p></o:p></span></p>
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            <p class="MsoNormal"><span style="font-family: Arial;"><a href="http://www.signaling-gateway.org/">http://www.signaling-gateway.org</a><o:p></o:p></span></p>
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            <p class="MsoNormal"><span style="font-family: Arial;">Signal transduction  knowledge environment<o:p></o:p></span></p>
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            <p class="MsoNormal"><span style="font-family: Arial;"><a href="http://stke.sciencemag.org/">http://stke.sciencemag.org</a><o:p></o:p></span></p>
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            <p class="MsoNormal"><span style="font-family: Arial;">Human protein reference  database<o:p></o:p></span></p>
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            <p class="MsoNormal"><span style="font-family: Arial;"><a href="http://www.hprd.org/">http://www.hprd.org</a><o:p></o:p></span></p>
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            <p class="MsoNormal"><span style="font-family: Arial;">GenMAPP<o:p></o:p></span></p>
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            <p class="MsoNormal"><span style="font-family: Arial;"><a href="http://www.genmapp.org/">http://www.genmapp.org</a><o:p></o:p></span></p>
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            <p class="MsoNormal"><span style="font-family: Arial;">KEGG<o:p></o:p></span></p>
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            <p class="MsoNormal"><span style="font-family: Arial;"><a href="http://www.genome.jp/kegg/">http://www.genome.jp/kegg/</a><o:p></o:p></span></p>
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            <p class="MsoNormal"><span style="font-family: Arial;">Gene ontology<o:p></o:p></span></p>
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            <p class="MsoNormal"><span style="font-family: Arial;"><a href="www.geneontology.org">http//www.geneontology.org</a><o:p></o:p></span></p>
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            <p class="MsoNormal"><span style="font-family: Arial;">Sigma-Aldrich pathways<o:p></o:p></span></p>
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            <p class="MsoNormal"><span style="font-family: Arial;"><a href="http://www.sigmaaldrich.com/Area_of_Interest/Biochemicals/Enzyme_Explorer/Key_Resources.html">http://www.sigmaaldrich.com/Area_of_Interest/Biochemicals/Enzyme_Explorer/Key_Resources.html</a><o:p></o:p></span></p>
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            <p class="MsoNormal"><span style="font-family: Arial;"><o:p>&nbsp;</o:p></span></p>
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        <tr style="height: 13.2pt;">
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            <p class="MsoNormal"><span style="font-family: Arial;">Gene arrays, BioScience  Corp<o:p></o:p></span></p>
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            <p class="MsoNormal"><span style="font-family: Arial;"><a href="http://www.superarray.com/">http://www.superarray.com</a><o:p></o:p></span></p>
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        <tr style="height: 27.45pt;">
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            <p class="MsoNormal"><span style="font-family: Arial;">Human cancer genome  anatomy consortium<o:p></o:p></span></p>
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            <p class="MsoNormal"><span style="font-family: Arial;"><a href="http://cgap.nci.nih.gov/">http://cgap.nci.nih.gov</a><o:p></o:p></span></p>
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        <tr style="height: 13.2pt;">
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            <p class="MsoNormal"><span style="font-family: Arial;">NetAffx<o:p></o:p></span></p>
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            <p class="MsoNormal"><span style="font-family: Arial;"><a href="http://www.affymetrix.com/index.affx">http://www.affymetrix.com/index.affx</a><o:p></o:p></span></p>
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    </tbody>
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</table>
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<p class="MsoNormal"><span style="font-family: Arial;"><o:p>&nbsp;</o:p></span></p>
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<p style="line-height: 150%;" class="MsoNormal">  </p>
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<em style=""><u><span style="font-family: Arial;">Biomedical literature</span></u></em><em style=""><span style="font-family: Arial;">: </span></em><span style="font-family: Arial;">Over the past few years, microarray studies have identified signatures of several important biological and clinical states (e.g. cancer metastasis, stem cell characteristics, drug resistance). These gene sets are valuable biological results. Unfortunately, because gene sets are typically published as tables in a paper, the </span><span style="line-height: 150%; font-family: Arial;">important biological findings they represent are not easily accessible to computational tools. <o:p></o:p>Our first goal was to convert published gene sets into an electronic form. Towards this we compiled a list of microarray articles with published gene expression signatures. From each article, we extracted one or more gene set from tables in the main text or supplementary information. Notably, our focus was on capturing the identity (e.g. gene symbol, GenBank accession) of all members in a gene set rather than on relationships between individual genes. </span><span style="font-family: Arial;">Currently the process of curating a gene set from the literature is largely manual. In this report we include a collection of 1181 gene sets curated in this manner from 343 distinct PubMed accessions.</span><span style="line-height: 150%; font-family: Arial;"></span>  <br />
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<p style="line-height: 150%;" class="MsoNormal">&nbsp;</p>
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<p style="line-height: 150%;" class="MsoNormal"><span style="font-weight: bold; color: rgb(255, 0, 0);">C3 (sequence motif gene sets)</span><span style="font-family: Arial;"><o:p></o:p></span></p>
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<p style="line-height: 150%;" class="MsoNormal"><span style="font-family: Arial; color: black;">We compiled gene sets on the basis of<span style="">&nbsp; </span>shared regulatory motifs from a recently published comparative analysis of the Human, Mouse, Rat and Dog genomes </span><!--[if supportFields]><span
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style='font-family:Arial;color:black'><span style='mso-element:field-begin'></span><span
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style='mso-spacerun:yes'> </span>ADDIN EN.CITE
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&lt;EndNote&gt;&lt;Cite&gt;&lt;Author&gt;Xie&lt;/Author&gt;&lt;Year&gt;2005&lt;/Year&gt;&lt;RecNum&gt;342&lt;/RecNum&gt;&lt;record&gt;&lt;database
 +
name='genesets_db.enl' path='C:\Local\xdev\active\msigdb\DOC_PUSH\genesets_db.enl'&gt;genesets_db.enl&lt;/database&gt;&lt;source-app
 +
name='EndNote' version='8.0'&gt;EndNote&lt;/source-app&gt;&lt;rec-number&gt;342&lt;/rec-number&gt;&lt;ref-type
 +
name='Journal
 +
Article'&gt;17&lt;/ref-type&gt;&lt;contributors&gt;&lt;authors&gt;&lt;author&gt;&lt;style
 +
face='normal' font='default' size='100%'&gt;Xie, X.&lt;/style&gt;&lt;/author&gt;&lt;author&gt;&lt;style
 +
face='normal' font='default' size='100%'&gt;Lu,
 +
J.&lt;/style&gt;&lt;/author&gt;&lt;author&gt;&lt;style face='normal'
 +
font='default' size='100%'&gt;Kulbokas, E.
 +
J.&lt;/style&gt;&lt;/author&gt;&lt;author&gt;&lt;style face='normal'
 +
font='default' size='100%'&gt;Golub, T. R.&lt;/style&gt;&lt;/author&gt;&lt;author&gt;&lt;style
 +
face='normal' font='default' size='100%'&gt;Mootha,
 +
V.&lt;/style&gt;&lt;/author&gt;&lt;author&gt;&lt;style face='normal'
 +
font='default' size='100%'&gt;Lindblad-Toh,
 +
K.&lt;/style&gt;&lt;/author&gt;&lt;author&gt;&lt;style face='normal'
 +
font='default' size='100%'&gt;Lander, E. S.&lt;/style&gt;&lt;/author&gt;&lt;author&gt;&lt;style
 +
face='normal' font='default' size='100%'&gt;Kellis,
 +
M.&lt;/style&gt;&lt;/author&gt;&lt;/authors&gt;&lt;/contributors&gt;&lt;auth-address&gt;&lt;style
 +
face='normal' font='default' size='100%'&gt;Broad Institute of MIT and Harvard,
 +
Cambridge, Massachusetts 02141, USA.&lt;/style&gt;&lt;/auth-address&gt;&lt;titles&gt;&lt;title&gt;&lt;style
 +
face='normal' font='default' size='100%'&gt;Systematic discovery of regulatory
 +
motifs in human promoters and 3&amp;apos; UTRs by comparison of several
 +
mammals&lt;/style&gt;&lt;/title&gt;&lt;secondary-title&gt;&lt;style
 +
face='normal' font='default' size='100%'&gt;Nature&lt;/style&gt;&lt;/secondary-title&gt;&lt;/titles&gt;&lt;periodical&gt;&lt;full-title&gt;&lt;style
 +
face='normal' font='default'
 +
size='100%'&gt;Nature&lt;/style&gt;&lt;/full-title&gt;&lt;/periodical&gt;&lt;pages&gt;&lt;style
 +
face='normal' font='default'
 +
size='100%'&gt;338-45&lt;/style&gt;&lt;/pages&gt;&lt;volume&gt;&lt;style
 +
face='normal' font='default' size='100%'&gt;434&lt;/style&gt;&lt;/volume&gt;&lt;number&gt;&lt;style
 +
face='normal' font='default'
 +
size='100%'&gt;7031&lt;/style&gt;&lt;/number&gt;&lt;keywords&gt;&lt;keyword&gt;&lt;style
 +
face='normal' font='default' size='100%'&gt;3&amp;apos; Untranslated
 +
Regions/*genetics&lt;/style&gt;&lt;/keyword&gt;&lt;keyword&gt;&lt;style
 +
face='normal' font='default' size='100%'&gt;Animals&lt;/style&gt;&lt;/keyword&gt;&lt;keyword&gt;&lt;style
 +
face='normal' font='default' size='100%'&gt;Base
 +
Sequence&lt;/style&gt;&lt;/keyword&gt;&lt;keyword&gt;&lt;style face='normal'
 +
font='default' size='100%'&gt;Comparative Study&lt;/style&gt;&lt;/keyword&gt;&lt;keyword&gt;&lt;style
 +
face='normal' font='default' size='100%'&gt;Conserved
 +
Sequence/genetics&lt;/style&gt;&lt;/keyword&gt;&lt;keyword&gt;&lt;style
 +
face='normal' font='default'
 +
size='100%'&gt;Dogs&lt;/style&gt;&lt;/keyword&gt;&lt;keyword&gt;&lt;style
 +
face='normal' font='default' size='100%'&gt;Gene Expression
 +
Profiling&lt;/style&gt;&lt;/keyword&gt;&lt;keyword&gt;&lt;style face='normal'
 +
font='default'
 +
size='100%'&gt;Humans&lt;/style&gt;&lt;/keyword&gt;&lt;keyword&gt;&lt;style
 +
face='normal' font='default'
 +
size='100%'&gt;Mammals/*genetics&lt;/style&gt;&lt;/keyword&gt;&lt;keyword&gt;&lt;style
 +
face='normal' font='default' size='100%'&gt;Mice&lt;/style&gt;&lt;/keyword&gt;&lt;keyword&gt;&lt;style
 +
face='normal' font='default'
 +
size='100%'&gt;MicroRNAs/genetics/metabolism&lt;/style&gt;&lt;/keyword&gt;&lt;keyword&gt;&lt;style
 +
face='normal' font='default' size='100%'&gt;Molecular Sequence
 +
Data&lt;/style&gt;&lt;/keyword&gt;&lt;keyword&gt;&lt;style face='normal'
 +
font='default' size='100%'&gt;Organ Specificity&lt;/style&gt;&lt;/keyword&gt;&lt;keyword&gt;&lt;style
 +
face='normal' font='default' size='100%'&gt;Promoter Regions
 +
(Genetics)/*genetics&lt;/style&gt;&lt;/keyword&gt;&lt;keyword&gt;&lt;style
 +
face='normal' font='default' size='100%'&gt;Rats&lt;/style&gt;&lt;/keyword&gt;&lt;keyword&gt;&lt;style
 +
face='normal' font='default' size='100%'&gt;Research Support, U.S.
 +
Gov&amp;apos;t, P.H.S.&lt;/style&gt;&lt;/keyword&gt;&lt;keyword&gt;&lt;style
 +
face='normal' font='default' size='100%'&gt;Sequence
 +
Alignment&lt;/style&gt;&lt;/keyword&gt;&lt;/keywords&gt;&lt;dates&gt;&lt;year&gt;&lt;style
 +
face='normal' font='default'
 +
size='100%'&gt;2005&lt;/style&gt;&lt;/year&gt;&lt;pub-dates&gt;&lt;date&gt;&lt;style
 +
face='normal' font='default' size='100%'&gt;Mar
 +
17&lt;/style&gt;&lt;/date&gt;&lt;/pub-dates&gt;&lt;/dates&gt;&lt;accession-num&gt;&lt;style
 +
face='normal' font='default'
 +
size='100%'&gt;15735639&lt;/style&gt;&lt;/accession-num&gt;&lt;urls&gt;&lt;related-urls&gt;&lt;url&gt;&lt;style
 +
face='normal' font='default' size='100%'&gt;http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?cmd=Retrieve&amp;amp;db=PubMed&amp;amp;dopt=Citation&amp;amp;list_uids=15735639<span
 +
style='mso-spacerun:yes'>
 +
</span>&lt;/style&gt;&lt;/url&gt;&lt;/related-urls&gt;&lt;/urls&gt;&lt;/record&gt;&lt;/Cite&gt;&lt;/EndNote&gt;<span
 +
style='mso-element:field-separator'></span></span><![endif]--><span style="font-family: Arial; color: black;">(Xie, Lu et al. 2005)</span><!--[if supportFields]><span
 +
style='font-family:Arial;color:black'><span style='mso-element:field-end'></span></span><![endif]--><span style="font-family: Arial; color: black;">. This database consists of 837 motifs sets including 222 microRNA target gene sets. <o:p></o:p></span></p>
 +
<br /><br /><span style="font-weight: bold; color: rgb(255, 0, 0);">C4 (computed gene sets)</span><br /><em style=""><span style="font-family: Arial;"></span></em><span style="font-family: Arial;"><br />We mined 4 expression compendia datasets for correlated gene sets by searching for neighbors (i.e. genes with similar expression profiles across a compendium) of <span style="">&nbsp;</span>380 cancer associated genes </span><!--[if supportFields]><span
 +
style='font-family:Arial'><span style='mso-element:field-begin'></span><span
 +
style='mso-spacerun:yes'> </span>ADDIN EN.CITE
 +
&lt;EndNote&gt;&lt;Cite&gt;&lt;Author&gt;Brentani&lt;/Author&gt;&lt;Year&gt;2003&lt;/Year&gt;&lt;RecNum&gt;184&lt;/RecNum&gt;&lt;record&gt;&lt;database
 +
name='genesets_db.enl' path='C:\Local\xdev\active\msigdb\DOC_PUSH\genesets_db.enl'&gt;genesets_db.enl&lt;/database&gt;&lt;source-app
 +
name='EndNote'
 +
version='8.0'&gt;EndNote&lt;/source-app&gt;&lt;rec-number&gt;184&lt;/rec-number&gt;&lt;ref-type
 +
name='Journal Article'&gt;17&lt;/ref-type&gt;&lt;contributors&gt;&lt;authors&gt;&lt;author&gt;&lt;style
 +
face='normal' font='default' size='100%'&gt;Brentani,
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H.&lt;/style&gt;&lt;/author&gt;&lt;author&gt;&lt;style face='normal'
 +
font='default' size='100%'&gt;Caballero, O.
 +
L.&lt;/style&gt;&lt;/author&gt;&lt;author&gt;&lt;style face='normal'
 +
font='default' size='100%'&gt;Camargo, A. A.&lt;/style&gt;&lt;/author&gt;&lt;author&gt;&lt;style
 +
face='normal' font='default' size='100%'&gt;da Silva, A.
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M.&lt;/style&gt;&lt;/author&gt;&lt;author&gt;&lt;style face='normal'
 +
font='default' size='100%'&gt;da Silva, W. A.,
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Jr.&lt;/style&gt;&lt;/author&gt;&lt;author&gt;&lt;style face='normal'
 +
font='default' size='100%'&gt;Dias Neto,
 +
E.&lt;/style&gt;&lt;/author&gt;&lt;author&gt;&lt;style face='normal' font='default'
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size='100%'&gt;Grivet, M.&lt;/style&gt;&lt;/author&gt;&lt;author&gt;&lt;style
 +
face='normal' font='default' size='100%'&gt;Gruber,
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A.&lt;/style&gt;&lt;/author&gt;&lt;author&gt;&lt;style face='normal'
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font='default' size='100%'&gt;Guimaraes, P. E.&lt;/style&gt;&lt;/author&gt;&lt;author&gt;&lt;style
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face='normal' font='default' size='100%'&gt;Hide,
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W.&lt;/style&gt;&lt;/author&gt;&lt;author&gt;&lt;style face='normal'
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font='default' size='100%'&gt;Iseli,
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C.&lt;/style&gt;&lt;/author&gt;&lt;author&gt;&lt;style face='normal'
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font='default' size='100%'&gt;Jongeneel, C. V.&lt;/style&gt;&lt;/author&gt;&lt;author&gt;&lt;style
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face='normal' font='default' size='100%'&gt;Kelso,
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J.&lt;/style&gt;&lt;/author&gt;&lt;author&gt;&lt;style face='normal'
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font='default' size='100%'&gt;Nagai, M.
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A.&lt;/style&gt;&lt;/author&gt;&lt;author&gt;&lt;style face='normal'
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font='default' size='100%'&gt;Ojopi, E. P.&lt;/style&gt;&lt;/author&gt;&lt;author&gt;&lt;style
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face='normal' font='default' size='100%'&gt;Osorio, E.
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C.&lt;/style&gt;&lt;/author&gt;&lt;author&gt;&lt;style face='normal'
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font='default' size='100%'&gt;Reis, E.
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M.&lt;/style&gt;&lt;/author&gt;&lt;author&gt;&lt;style face='normal'
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font='default' size='100%'&gt;Riggins, G. J.&lt;/style&gt;&lt;/author&gt;&lt;author&gt;&lt;style
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face='normal' font='default' size='100%'&gt;Simpson, A.
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J.&lt;/style&gt;&lt;/author&gt;&lt;author&gt;&lt;style face='normal'
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font='default' size='100%'&gt;de Souza,
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S.&lt;/style&gt;&lt;/author&gt;&lt;author&gt;&lt;style face='normal'
 +
font='default' size='100%'&gt;Stevenson, B. J.&lt;/style&gt;&lt;/author&gt;&lt;author&gt;&lt;style
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face='normal' font='default' size='100%'&gt;Strausberg, R.
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L.&lt;/style&gt;&lt;/author&gt;&lt;author&gt;&lt;style face='normal'
 +
font='default' size='100%'&gt;Tajara, E.
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H.&lt;/style&gt;&lt;/author&gt;&lt;author&gt;&lt;style face='normal'
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font='default' size='100%'&gt;Verjovski-Almeida,
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S.&lt;/style&gt;&lt;/author&gt;&lt;author&gt;&lt;style face='normal'
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L.&lt;/style&gt;&lt;/author&gt;&lt;author&gt;&lt;style face='normal'
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H.&lt;/style&gt;&lt;/author&gt;&lt;author&gt;&lt;style face='normal'
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F.&lt;/style&gt;&lt;/author&gt;&lt;author&gt;&lt;style face='normal'
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font='default' size='100%'&gt;Bodmer, W.
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F.&lt;/style&gt;&lt;/author&gt;&lt;author&gt;&lt;style face='normal'
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R.&lt;/style&gt;&lt;/author&gt;&lt;author&gt;&lt;style face='normal'
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font='default' size='100%'&gt;Camargo, L.
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P.&lt;/style&gt;&lt;/author&gt;&lt;author&gt;&lt;style face='normal'
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font='default' size='100%'&gt;Cavenee,
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W.&lt;/style&gt;&lt;/author&gt;&lt;author&gt;&lt;style face='normal'
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font='default' size='100%'&gt;Cerutti, J.
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M.&lt;/style&gt;&lt;/author&gt;&lt;author&gt;&lt;style face='normal'
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font='default' size='100%'&gt;Coelho Andrade, L.
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E.&lt;/style&gt;&lt;/author&gt;&lt;author&gt;&lt;style face='normal'
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font='default' size='100%'&gt;Costa dos Santos, P.
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C.&lt;/style&gt;&lt;/author&gt;&lt;author&gt;&lt;style face='normal'
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font='default' size='100%'&gt;Ramos Costa, M.
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C.&lt;/style&gt;&lt;/author&gt;&lt;author&gt;&lt;style face='normal'
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font='default' size='100%'&gt;da Silva, I. T.&lt;/style&gt;&lt;/author&gt;&lt;author&gt;&lt;style
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face='normal' font='default' size='100%'&gt;Estecio, M.
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R.&lt;/style&gt;&lt;/author&gt;&lt;author&gt;&lt;style face='normal'
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font='default' size='100%'&gt;Sa Ferreira,
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K.&lt;/style&gt;&lt;/author&gt;&lt;author&gt;&lt;style face='normal'
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font='default' size='100%'&gt;Furnari, F. B.&lt;/style&gt;&lt;/author&gt;&lt;author&gt;&lt;style
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face='normal' font='default' size='100%'&gt;Faria, M.,
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Jr.&lt;/style&gt;&lt;/author&gt;&lt;author&gt;&lt;style face='normal'
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font='default' size='100%'&gt;Galante, P. A.&lt;/style&gt;&lt;/author&gt;&lt;author&gt;&lt;style
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face='normal' font='default' size='100%'&gt;Guimaraes, G.
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S.&lt;/style&gt;&lt;/author&gt;&lt;author&gt;&lt;style face='normal'
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font='default' size='100%'&gt;Holanda, A.
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J.&lt;/style&gt;&lt;/author&gt;&lt;author&gt;&lt;style face='normal'
 +
font='default' size='100%'&gt;Kimura, E. T.&lt;/style&gt;&lt;/author&gt;&lt;author&gt;&lt;style
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face='normal' font='default' size='100%'&gt;Leerkes, M.
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R.&lt;/style&gt;&lt;/author&gt;&lt;author&gt;&lt;style face='normal'
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font='default' size='100%'&gt;Lu,
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X.&lt;/style&gt;&lt;/author&gt;&lt;author&gt;&lt;style face='normal'
 +
font='default' size='100%'&gt;Maciel, R. M.&lt;/style&gt;&lt;/author&gt;&lt;author&gt;&lt;style
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face='normal' font='default' size='100%'&gt;Martins, E.
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A.&lt;/style&gt;&lt;/author&gt;&lt;author&gt;&lt;style face='normal'
 +
font='default' size='100%'&gt;Massirer, K.
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B.&lt;/style&gt;&lt;/author&gt;&lt;author&gt;&lt;style face='normal'
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font='default' size='100%'&gt;Melo, A. S.&lt;/style&gt;&lt;/author&gt;&lt;author&gt;&lt;style
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face='normal' font='default' size='100%'&gt;Mestriner, C.
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A.&lt;/style&gt;&lt;/author&gt;&lt;author&gt;&lt;style face='normal'
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font='default' size='100%'&gt;Miracca, E.
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C.&lt;/style&gt;&lt;/author&gt;&lt;author&gt;&lt;style face='normal'
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font='default' size='100%'&gt;Miranda, L. L.&lt;/style&gt;&lt;/author&gt;&lt;author&gt;&lt;style
 +
face='normal' font='default' size='100%'&gt;Nobrega, F.
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G.&lt;/style&gt;&lt;/author&gt;&lt;author&gt;&lt;style face='normal'
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font='default' size='100%'&gt;Oliveira, P.
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S.&lt;/style&gt;&lt;/author&gt;&lt;author&gt;&lt;style face='normal'
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font='default' size='100%'&gt;Paquola, A. C.&lt;/style&gt;&lt;/author&gt;&lt;author&gt;&lt;style
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face='normal' font='default' size='100%'&gt;Pandolfi, J.
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R.&lt;/style&gt;&lt;/author&gt;&lt;author&gt;&lt;style face='normal'
 +
font='default' size='100%'&gt;Campos Pardini, M.
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I.&lt;/style&gt;&lt;/author&gt;&lt;author&gt;&lt;style face='normal'
 +
font='default' size='100%'&gt;Passetti, F.&lt;/style&gt;&lt;/author&gt;&lt;author&gt;&lt;style
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face='normal' font='default' size='100%'&gt;Quackenbush,
 +
J.&lt;/style&gt;&lt;/author&gt;&lt;author&gt;&lt;style face='normal'
 +
font='default' size='100%'&gt;Schnabel,
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B.&lt;/style&gt;&lt;/author&gt;&lt;author&gt;&lt;style face='normal'
 +
font='default' size='100%'&gt;Sogayar, M.
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C.&lt;/style&gt;&lt;/author&gt;&lt;author&gt;&lt;style face='normal' font='default'
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size='100%'&gt;Souza, J. E.&lt;/style&gt;&lt;/author&gt;&lt;author&gt;&lt;style
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face='normal' font='default' size='100%'&gt;Valentini, S.
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R.&lt;/style&gt;&lt;/author&gt;&lt;author&gt;&lt;style face='normal'
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font='default' size='100%'&gt;Zaiats, A.
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C.&lt;/style&gt;&lt;/author&gt;&lt;author&gt;&lt;style face='normal'
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font='default' size='100%'&gt;Amaral, E.
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J.&lt;/style&gt;&lt;/author&gt;&lt;author&gt;&lt;style face='normal'
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font='default' size='100%'&gt;Arnaldi, L.
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A.&lt;/style&gt;&lt;/author&gt;&lt;author&gt;&lt;style face='normal'
 +
font='default' size='100%'&gt;de Araujo, A.
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G.&lt;/style&gt;&lt;/author&gt;&lt;author&gt;&lt;style face='normal'
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font='default' size='100%'&gt;de Bessa, S.
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A.&lt;/style&gt;&lt;/author&gt;&lt;author&gt;&lt;style face='normal'
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font='default' size='100%'&gt;Bicknell, D.
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C.&lt;/style&gt;&lt;/author&gt;&lt;author&gt;&lt;style face='normal'
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E.&lt;/style&gt;&lt;/author&gt;&lt;author&gt;&lt;style face='normal'
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font='default' size='100%'&gt;Carraro, D.
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M.&lt;/style&gt;&lt;/author&gt;&lt;author&gt;&lt;style face='normal'
 +
font='default' size='100%'&gt;Carrer,
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H.&lt;/style&gt;&lt;/author&gt;&lt;author&gt;&lt;style face='normal' font='default'
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size='100%'&gt;Carvalho, A. F.&lt;/style&gt;&lt;/author&gt;&lt;author&gt;&lt;style
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face='normal' font='default' size='100%'&gt;Colin,
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C.&lt;/style&gt;&lt;/author&gt;&lt;author&gt;&lt;style face='normal'
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font='default' size='100%'&gt;Costa,
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F.&lt;/style&gt;&lt;/author&gt;&lt;author&gt;&lt;style face='normal' font='default'
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size='100%'&gt;Curcio, C.&lt;/style&gt;&lt;/author&gt;&lt;author&gt;&lt;style
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face='normal' font='default' size='100%'&gt;Guerreiro da Silva, I.
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D.&lt;/style&gt;&lt;/author&gt;&lt;author&gt;&lt;style face='normal'
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font='default' size='100%'&gt;Pereira da Silva,
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N.&lt;/style&gt;&lt;/author&gt;&lt;author&gt;&lt;style face='normal'
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font='default' size='100%'&gt;Dellamano, M.&lt;/style&gt;&lt;/author&gt;&lt;author&gt;&lt;style
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face='normal' font='default' size='100%'&gt;El-Dorry,
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H.&lt;/style&gt;&lt;/author&gt;&lt;author&gt;&lt;style face='normal'
 +
font='default' size='100%'&gt;Espreafico, E.
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M.&lt;/style&gt;&lt;/author&gt;&lt;author&gt;&lt;style face='normal'
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font='default' size='100%'&gt;Scattone Ferreira, A.
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J.&lt;/style&gt;&lt;/author&gt;&lt;author&gt;&lt;style face='normal'
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font='default' size='100%'&gt;Ayres Ferreira,
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C.&lt;/style&gt;&lt;/author&gt;&lt;author&gt;&lt;style face='normal'
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H.&lt;/style&gt;&lt;/author&gt;&lt;author&gt;&lt;style face='normal'
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font='default' size='100%'&gt;Giannella-Neto,
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D.&lt;/style&gt;&lt;/author&gt;&lt;author&gt;&lt;style face='normal'
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font='default' size='100%'&gt;Giannella, M. L.&lt;/style&gt;&lt;/author&gt;&lt;author&gt;&lt;style
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face='normal' font='default' size='100%'&gt;Giorgi, R.
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R.&lt;/style&gt;&lt;/author&gt;&lt;author&gt;&lt;style face='normal'
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font='default' size='100%'&gt;Goldman, G.
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H.&lt;/style&gt;&lt;/author&gt;&lt;author&gt;&lt;style face='normal'
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C.&lt;/style&gt;&lt;/author&gt;&lt;author&gt;&lt;style face='normal'
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L.&lt;/style&gt;&lt;/author&gt;&lt;author&gt;&lt;style face='normal'
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face='normal' font='default' size='100%'&gt;Kowalski, L.
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P.&lt;/style&gt;&lt;/author&gt;&lt;author&gt;&lt;style face='normal'
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font='default' size='100%'&gt;Krieger, J.
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E.&lt;/style&gt;&lt;/author&gt;&lt;author&gt;&lt;style face='normal'
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A.&lt;/style&gt;&lt;/author&gt;&lt;author&gt;&lt;style face='normal'
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font='default' size='100%'&gt;Luna, A.
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M.&lt;/style&gt;&lt;/author&gt;&lt;author&gt;&lt;style face='normal'
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font='default' size='100%'&gt;Mackay, A.&lt;/style&gt;&lt;/author&gt;&lt;author&gt;&lt;style
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face='normal' font='default' size='100%'&gt;Mari, S.
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K.&lt;/style&gt;&lt;/author&gt;&lt;author&gt;&lt;style face='normal'
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A.&lt;/style&gt;&lt;/author&gt;&lt;author&gt;&lt;style face='normal'
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font='default' size='100%'&gt;Martins, W. K.&lt;/style&gt;&lt;/author&gt;&lt;author&gt;&lt;style
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face='normal' font='default' size='100%'&gt;Montagnini,
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A.&lt;/style&gt;&lt;/author&gt;&lt;author&gt;&lt;style face='normal'
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M.&lt;/style&gt;&lt;/author&gt;&lt;author&gt;&lt;style face='normal'
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font='default' size='100%'&gt;Nascimento, A. L.&lt;/style&gt;&lt;/author&gt;&lt;author&gt;&lt;style
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M.&lt;/style&gt;&lt;/author&gt;&lt;author&gt;&lt;style face='normal'
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font='default' size='100%'&gt;Nobrega, M.
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P.&lt;/style&gt;&lt;/author&gt;&lt;author&gt;&lt;style face='normal'
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J.&lt;/style&gt;&lt;/author&gt;&lt;author&gt;&lt;style face='normal'
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Y.&lt;/style&gt;&lt;/author&gt;&lt;author&gt;&lt;style face='normal'
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font='default' size='100%'&gt;Ruas de Melo, A.
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I.&lt;/style&gt;&lt;/author&gt;&lt;author&gt;&lt;style face='normal'
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L.&lt;/style&gt;&lt;/author&gt;&lt;author&gt;&lt;style face='normal'
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font='default' size='100%'&gt;Guimaraes Pereira,
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G.&lt;/style&gt;&lt;/author&gt;&lt;author&gt;&lt;style face='normal'
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B.&lt;/style&gt;&lt;/author&gt;&lt;author&gt;&lt;style face='normal' font='default'
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size='100%'&gt;Pessoa, J. G.&lt;/style&gt;&lt;/author&gt;&lt;author&gt;&lt;style
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P.&lt;/style&gt;&lt;/author&gt;&lt;author&gt;&lt;style face='normal'
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font='default' size='100%'&gt;Rainho, C.
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A.&lt;/style&gt;&lt;/author&gt;&lt;author&gt;&lt;style face='normal' font='default'
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size='100%'&gt;Rodrigues, V.&lt;/style&gt;&lt;/author&gt;&lt;author&gt;&lt;style
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face='normal' font='default' size='100%'&gt;Rogatto, S.
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R.&lt;/style&gt;&lt;/author&gt;&lt;author&gt;&lt;style face='normal'
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font='default' size='100%'&gt;Romano, C.
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M.&lt;/style&gt;&lt;/author&gt;&lt;author&gt;&lt;style face='normal' font='default'
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size='100%'&gt;Romeiro, J. G.&lt;/style&gt;&lt;/author&gt;&lt;author&gt;&lt;style
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face='normal' font='default' size='100%'&gt;Rossi, B.
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M.&lt;/style&gt;&lt;/author&gt;&lt;author&gt;&lt;style face='normal'
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font='default' size='100%'&gt;Rusticci,
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M.&lt;/style&gt;&lt;/author&gt;&lt;author&gt;&lt;style face='normal' font='default'
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size='100%'&gt;Guerra de Sa, R.&lt;/style&gt;&lt;/author&gt;&lt;author&gt;&lt;style
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C.&lt;/style&gt;&lt;/author&gt;&lt;author&gt;&lt;style face='normal'
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L.&lt;/style&gt;&lt;/author&gt;&lt;author&gt;&lt;style face='normal'
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font='default' size='100%'&gt;Silva, T. C.&lt;/style&gt;&lt;/author&gt;&lt;author&gt;&lt;style
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face='normal' font='default' size='100%'&gt;Soares, F.
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A.&lt;/style&gt;&lt;/author&gt;&lt;author&gt;&lt;style face='normal'
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font='default' size='100%'&gt;Sonati Mde,
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F.&lt;/style&gt;&lt;/author&gt;&lt;author&gt;&lt;style face='normal'
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J.&lt;/style&gt;&lt;/author&gt;&lt;author&gt;&lt;style face='normal'
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font='default' size='100%'&gt;Queiroz,
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D.&lt;/style&gt;&lt;/author&gt;&lt;author&gt;&lt;style face='normal'
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font='default' size='100%'&gt;Valente, V.&lt;/style&gt;&lt;/author&gt;&lt;author&gt;&lt;style
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face='normal' font='default' size='100%'&gt;Vettore, A.
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font='default' size='100%'&gt;Villanova, F.
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font='default' size='100%'&gt;Zago, M. A.&lt;/style&gt;&lt;/author&gt;&lt;author&gt;&lt;style
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face='normal' font='default' size='100%'&gt;Zalcberg,
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H.&lt;/style&gt;&lt;/author&gt;&lt;/authors&gt;&lt;/contributors&gt;&lt;auth-address&gt;&lt;style
 +
face='normal' font='default' size='100%'&gt;Laboratorio de Genetica Molecular
 +
do Cancer, Departmento de Radiologia, Universidade de Sao Paulo, Travessa da
 +
Rua Dr. Ovideo Pires de Campos S/N, 4deg,
 +
Brazil.&lt;/style&gt;&lt;/auth-address&gt;&lt;titles&gt;&lt;title&gt;&lt;style
 +
face='normal' font='default' size='100%'&gt;The generation and utilization of a
 +
cancer-oriented representation of the human transcriptome by using expressed
 +
sequence tags&lt;/style&gt;&lt;/title&gt;&lt;secondary-title&gt;&lt;style
 +
face='normal' font='default' size='100%'&gt;Proc Natl Acad Sci U S
 +
A&lt;/style&gt;&lt;/secondary-title&gt;&lt;/titles&gt;&lt;periodical&gt;&lt;full-title&gt;&lt;style
 +
face='normal' font='default' size='100%'&gt;Proc Natl Acad Sci U S A&lt;/style&gt;&lt;/full-title&gt;&lt;/periodical&gt;&lt;pages&gt;&lt;style
 +
face='normal' font='default'
 +
size='100%'&gt;13418-23&lt;/style&gt;&lt;/pages&gt;&lt;volume&gt;&lt;style
 +
face='normal' font='default'
 +
size='100%'&gt;100&lt;/style&gt;&lt;/volume&gt;&lt;number&gt;&lt;style
 +
face='normal' font='default' size='100%'&gt;23&lt;/style&gt;&lt;/number&gt;&lt;keywords&gt;&lt;keyword&gt;&lt;style
 +
face='normal' font='default' size='100%'&gt;Chromosome
 +
Mapping&lt;/style&gt;&lt;/keyword&gt;&lt;keyword&gt;&lt;style face='normal'
 +
font='default' size='100%'&gt;Databases,
 +
Genetic&lt;/style&gt;&lt;/keyword&gt;&lt;keyword&gt;&lt;style face='normal'
 +
font='default' size='100%'&gt;*Expressed Sequence
 +
Tags&lt;/style&gt;&lt;/keyword&gt;&lt;keyword&gt;&lt;style face='normal'
 +
font='default' size='100%'&gt;*Gene Expression Regulation,
 +
Neoplastic&lt;/style&gt;&lt;/keyword&gt;&lt;keyword&gt;&lt;style face='normal'
 +
font='default'
 +
size='100%'&gt;Humans&lt;/style&gt;&lt;/keyword&gt;&lt;keyword&gt;&lt;style
 +
face='normal' font='default' size='100%'&gt;Neoplasms/*genetics/metabolism&lt;/style&gt;&lt;/keyword&gt;&lt;keyword&gt;&lt;style
 +
face='normal' font='default' size='100%'&gt;Polymorphism, Single
 +
Nucleotide&lt;/style&gt;&lt;/keyword&gt;&lt;keyword&gt;&lt;style face='normal'
 +
font='default' size='100%'&gt;*Proteome&lt;/style&gt;&lt;/keyword&gt;&lt;keyword&gt;&lt;style
 +
face='normal' font='default' size='100%'&gt;RNA,
 +
Messenger/*metabolism&lt;/style&gt;&lt;/keyword&gt;&lt;keyword&gt;&lt;style
 +
face='normal' font='default' size='100%'&gt;Research Support, Non-U.S.
 +
Gov&amp;apos;t&lt;/style&gt;&lt;/keyword&gt;&lt;keyword&gt;&lt;style
 +
face='normal' font='default' size='100%'&gt;Tissue Distribution&lt;/style&gt;&lt;/keyword&gt;&lt;keyword&gt;&lt;style
 +
face='normal' font='default' size='100%'&gt;Variation
 +
(Genetics)&lt;/style&gt;&lt;/keyword&gt;&lt;/keywords&gt;&lt;dates&gt;&lt;year&gt;&lt;style
 +
face='normal' font='default' size='100%'&gt;2003&lt;/style&gt;&lt;/year&gt;&lt;pub-dates&gt;&lt;date&gt;&lt;style
 +
face='normal' font='default' size='100%'&gt;Nov
 +
11&lt;/style&gt;&lt;/date&gt;&lt;/pub-dates&gt;&lt;/dates&gt;&lt;accession-num&gt;&lt;style
 +
face='normal' font='default'
 +
size='100%'&gt;14593198&lt;/style&gt;&lt;/accession-num&gt;&lt;urls&gt;&lt;related-urls&gt;&lt;url&gt;&lt;style
 +
face='normal' font='default' size='100%'&gt;http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?cmd=Retrieve&amp;amp;db=PubMed&amp;amp;dopt=Citation&amp;amp;list_uids=14593198
 +
&lt;/style&gt;&lt;/url&gt;&lt;/related-urls&gt;&lt;/urls&gt;&lt;/record&gt;&lt;/Cite&gt;&lt;/EndNote&gt;<span
 +
style='mso-element:field-separator'></span></span><![endif]--><span style="font-family: Arial;">(Brentani, Caballero et al. 2003)</span><!--[if supportFields]><span
 +
style='font-family:Arial'><span style='mso-element:field-end'></span></span><![endif]--><span style="font-family: Arial;">. Neighborhoods with &lt;25 genes at a Pearson correlation threshold of 0.8 were omitted yielding 427 sets. This category of the database is identical to that previously reported in <span style="">&nbsp;</span></span><!--[if supportFields]><span
 +
style='font-family:Arial'><span style='mso-element:field-begin'></span><span
 +
style='mso-spacerun:yes'> </span>ADDIN EN.CITE
 +
&lt;EndNote&gt;&lt;Cite&gt;&lt;Author&gt;Subramanian&lt;/Author&gt;&lt;Year&gt;2005&lt;/Year&gt;&lt;RecNum&gt;369&lt;/RecNum&gt;&lt;record&gt;&lt;database
 +
name=&quot;genesets_db.enl&quot; path=&quot;C:\Local\xdev\active\msigdb\DOC_PUSH\genesets_db.enl&quot;&gt;genesets_db.enl&lt;/database&gt;&lt;source-app
 +
name=&quot;EndNote&quot;
 +
version=&quot;8.0&quot;&gt;EndNote&lt;/source-app&gt;&lt;rec-number&gt;369&lt;/rec-number&gt;&lt;ref-type
 +
name=&quot;Journal
 +
Article&quot;&gt;17&lt;/ref-type&gt;&lt;contributors&gt;&lt;authors&gt;&lt;author&gt;&lt;style
 +
face=&quot;normal&quot; font=&quot;default&quot;
 +
size=&quot;100%&quot;&gt;Subramanian,
 +
A.&lt;/style&gt;&lt;/author&gt;&lt;author&gt;&lt;style face=&quot;normal&quot;
 +
font=&quot;default&quot; size=&quot;100%&quot;&gt;Tamayo,
 +
P.&lt;/style&gt;&lt;/author&gt;&lt;author&gt;&lt;style face=&quot;normal&quot;
 +
font=&quot;default&quot; size=&quot;100%&quot;&gt;Mootha, V.
 +
K.&lt;/style&gt;&lt;/author&gt;&lt;author&gt;&lt;style face=&quot;normal&quot;
 +
font=&quot;default&quot; size=&quot;100%&quot;&gt;Mukherjee,
 +
S.&lt;/style&gt;&lt;/author&gt;&lt;author&gt;&lt;style face=&quot;normal&quot;
 +
font=&quot;default&quot; size=&quot;100%&quot;&gt;Ebert, B.
 +
L.&lt;/style&gt;&lt;/author&gt;&lt;author&gt;&lt;style face=&quot;normal&quot;
 +
font=&quot;default&quot; size=&quot;100%&quot;&gt;Gillette, M.
 +
A.&lt;/style&gt;&lt;/author&gt;&lt;author&gt;&lt;style face=&quot;normal&quot;
 +
font=&quot;default&quot; size=&quot;100%&quot;&gt;Paulovich,
 +
A.&lt;/style&gt;&lt;/author&gt;&lt;author&gt;&lt;style face=&quot;normal&quot;
 +
font=&quot;default&quot; size=&quot;100%&quot;&gt;Pomeroy, S.
 +
L.&lt;/style&gt;&lt;/author&gt;&lt;author&gt;&lt;style face=&quot;normal&quot;
 +
font=&quot;default&quot; size=&quot;100%&quot;&gt;Golub, T.
 +
R.&lt;/style&gt;&lt;/author&gt;&lt;author&gt;&lt;style face=&quot;normal&quot;
 +
font=&quot;default&quot; size=&quot;100%&quot;&gt;Lander, E.
 +
S.&lt;/style&gt;&lt;/author&gt;&lt;author&gt;&lt;style face=&quot;normal&quot;
 +
font=&quot;default&quot; size=&quot;100%&quot;&gt;Mesirov, J.
 +
P.&lt;/style&gt;&lt;/author&gt;&lt;/authors&gt;&lt;/contributors&gt;&lt;auth-address&gt;&lt;style
 +
face=&quot;normal&quot; font=&quot;default&quot; size=&quot;100%&quot;&gt;Broad
 +
Institute of Massachusetts Institute of Technology and Harvard, 320 Charles
 +
Street, Cambridge, MA
 +
02141.&lt;/style&gt;&lt;/auth-address&gt;&lt;titles&gt;&lt;title&gt;&lt;style
 +
face=&quot;normal&quot; font=&quot;default&quot; size=&quot;100%&quot;&gt;From
 +
the Cover: Gene set enrichment analysis: A knowledge-based approach for
 +
interpreting genome-wide expression
 +
profiles&lt;/style&gt;&lt;/title&gt;&lt;secondary-title&gt;&lt;style
 +
face=&quot;normal&quot; font=&quot;default&quot; size=&quot;100%&quot;&gt;Proc
 +
Natl Acad Sci U S A&lt;/style&gt;&lt;/secondary-title&gt;&lt;/titles&gt;&lt;periodical&gt;&lt;full-title&gt;&lt;style
 +
face=&quot;normal&quot; font=&quot;default&quot; size=&quot;100%&quot;&gt;Proc
 +
Natl Acad Sci U S
 +
A&lt;/style&gt;&lt;/full-title&gt;&lt;/periodical&gt;&lt;pages&gt;&lt;style
 +
face=&quot;normal&quot; font=&quot;default&quot;
 +
size=&quot;100%&quot;&gt;15545-50&lt;/style&gt;&lt;/pages&gt;&lt;volume&gt;&lt;style
 +
face=&quot;normal&quot; font=&quot;default&quot;
 +
size=&quot;100%&quot;&gt;102&lt;/style&gt;&lt;/volume&gt;&lt;number&gt;&lt;style
 +
face=&quot;normal&quot; font=&quot;default&quot;
 +
size=&quot;100%&quot;&gt;43&lt;/style&gt;&lt;/number&gt;&lt;dates&gt;&lt;year&gt;&lt;style
 +
face=&quot;normal&quot; font=&quot;default&quot;
 +
size=&quot;100%&quot;&gt;2005&lt;/style&gt;&lt;/year&gt;&lt;pub-dates&gt;&lt;date&gt;&lt;style
 +
face=&quot;normal&quot; font=&quot;default&quot; size=&quot;100%&quot;&gt;Oct
 +
25&lt;/style&gt;&lt;/date&gt;&lt;/pub-dates&gt;&lt;/dates&gt;&lt;accession-num&gt;&lt;style
 +
face=&quot;normal&quot; font=&quot;default&quot;
 +
size=&quot;100%&quot;&gt;16199517&lt;/style&gt;&lt;/accession-num&gt;&lt;urls&gt;&lt;related-urls&gt;&lt;url&gt;&lt;style
 +
face=&quot;normal&quot; font=&quot;default&quot;
 +
size=&quot;100%&quot;&gt;http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?cmd=Retrieve&amp;amp;db=PubMed&amp;amp;dopt=Citation&amp;amp;list_uids=16199517<span
 +
style='mso-spacerun:yes'>  </span>&lt;/style&gt;&lt;/url&gt;&lt;/related-urls&gt;&lt;/urls&gt;&lt;/record&gt;&lt;/Cite&gt;&lt;/EndNote&gt;<span
 +
style='mso-element:field-separator'></span></span><![endif]--><span style="font-family: Arial;">(Subramanian, Tamayo et al. 2005)</span><!--[if supportFields]><span
 +
style='font-family:Arial'><span style='mso-element:field-end'></span></span><![endif]--><span style="font-family: Arial;">.</span><span style="font-size: 11pt; line-height: 150%; font-family: Arial;"><o:p></o:p></span>  <br /><br />

Revision as of 19:12, 15 December 2006


Details on how the gene set databases were generated is provided below:

C1 (Positional gene sets)

Cytogenetic locations were parsed from hugo and entrez (release x). When there were conflicts, the Entrez entry was used.


C2 (Curated gene sets)

C2 sets were curated from several sources including:

Online pathway databases: Several online resources provide catalogs of well studied metabolic and signaling pathways as well as functional categories of genes. We downloaded gene sets from 12 such databases into our system.

<o:p> </o:p>

<tbody> </tbody>

NAME<o:p></o:p>

URL / REFERENCE<o:p></o:p>

BioCarta<o:p></o:p>

<a href="http://www.biocarta.com/">http://www.biocarta.com</a><o:p></o:p>

Signaling pathway database<o:p></o:p>

<a href="http://www.grt.kyushu-u.ac.jp/spad/menu.html">http://www.grt.kyushu-u.ac.jp/spad/menu.html</a><o:p></o:p>

Signaling gateway<o:p></o:p>

<a href="http://www.signaling-gateway.org/">http://www.signaling-gateway.org</a><o:p></o:p>

Signal transduction knowledge environment<o:p></o:p>

<a href="http://stke.sciencemag.org/">http://stke.sciencemag.org</a><o:p></o:p>

Human protein reference database<o:p></o:p>

<a href="http://www.hprd.org/">http://www.hprd.org</a><o:p></o:p>

GenMAPP<o:p></o:p>

<a href="http://www.genmapp.org/">http://www.genmapp.org</a><o:p></o:p>

KEGG<o:p></o:p>

<a href="http://www.genome.jp/kegg/">http://www.genome.jp/kegg/</a><o:p></o:p>

Gene ontology<o:p></o:p>

<a href="www.geneontology.org">http//www.geneontology.org</a><o:p></o:p>

Sigma-Aldrich pathways<o:p></o:p>

<a href="http://www.sigmaaldrich.com/Area_of_Interest/Biochemicals/Enzyme_Explorer/Key_Resources.html">http://www.sigmaaldrich.com/Area_of_Interest/Biochemicals/Enzyme_Explorer/Key_Resources.html</a><o:p></o:p>

<o:p> </o:p>

Gene arrays, BioScience Corp<o:p></o:p>

<a href="http://www.superarray.com/">http://www.superarray.com</a><o:p></o:p>

Human cancer genome anatomy consortium<o:p></o:p>

<a href="http://cgap.nci.nih.gov/">http://cgap.nci.nih.gov</a><o:p></o:p>

NetAffx<o:p></o:p>

<a href="http://www.affymetrix.com/index.affx">http://www.affymetrix.com/index.affx</a><o:p></o:p>

<o:p> </o:p>

Biomedical literature: Over the past few years, microarray studies have identified signatures of several important biological and clinical states (e.g. cancer metastasis, stem cell characteristics, drug resistance). These gene sets are valuable biological results. Unfortunately, because gene sets are typically published as tables in a paper, the important biological findings they represent are not easily accessible to computational tools. <o:p></o:p>Our first goal was to convert published gene sets into an electronic form. Towards this we compiled a list of microarray articles with published gene expression signatures. From each article, we extracted one or more gene set from tables in the main text or supplementary information. Notably, our focus was on capturing the identity (e.g. gene symbol, GenBank accession) of all members in a gene set rather than on relationships between individual genes. Currently the process of curating a gene set from the literature is largely manual. In this report we include a collection of 1181 gene sets curated in this manner from 343 distinct PubMed accessions.

 

C3 (sequence motif gene sets)<o:p></o:p>

We compiled gene sets on the basis of  shared regulatory motifs from a recently published comparative analysis of the Human, Mouse, Rat and Dog genomes (Xie, Lu et al. 2005). This database consists of 837 motifs sets including 222 microRNA target gene sets. <o:p></o:p>



C4 (computed gene sets)

We mined 4 expression compendia datasets for correlated gene sets by searching for neighbors (i.e. genes with similar expression profiles across a compendium) of  380 cancer associated genes
(Brentani, Caballero et al. 2003). Neighborhoods with <25 genes at a Pearson correlation threshold of 0.8 were omitted yielding 427 sets. This category of the database is identical to that previously reported in  (Subramanian, Tamayo et al. 2005).<o:p></o:p>

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