QAing UCSC Genes: Difference between revisions

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(Gene Sorter column sources.)
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[[Image:hg19uc002ypa.2.pdf|testing]]
[[Image:hg19uc002ypa.2.pdf|testing]]
<table class=MsoNormalTable border=1 cellspacing=0 cellpadding=0 width=770
style='width:577.5pt;mso-cellspacing:0in;background:#FFFEE8'>
<tr style='mso-yfti-irow:0;mso-yfti-firstrow:yes'>
  <td style='background:#D9E4F8;padding:.75pt .75pt .75pt .75pt'>
  <p class=MsoNormal><b>Name</b></p>
  </td>
  <td width=434 style='width:325.25pt;background:#D9E4F8;padding:.75pt .75pt .75pt .75pt'>
  <p class=MsoNormal><b>Description</b></p>
  </td>
  <td width=229 style='width:171.75pt;background:#D9E4F8;padding:.75pt .75pt .75pt .75pt'>
  <p class=MsoNormal><b>Source</b></p>
  </td>
</tr>
<tr style='mso-yfti-irow:1'>
  <td style='padding:.75pt .75pt .75pt .75pt'>
  <p class=MsoNormal>#</p>
  </td>
  <td width=434 style='width:325.25pt;padding:.75pt .75pt .75pt .75pt'>
  <p class=MsoNormal>Item Number in Displayed List/Select Gene</p>
  </td>
  <td width=229 style='width:171.75pt;padding:.75pt .75pt .75pt .75pt'>
  <p class=MsoNormal>n/a</p>
  </td>
</tr>
<tr style='mso-yfti-irow:2'>
  <td style='padding:.75pt .75pt .75pt .75pt'>
  <p class=MsoNormal>Name</p>
  </td>
  <td width=434 style='width:325.25pt;padding:.75pt .75pt .75pt .75pt'>
  <p class=MsoNormal>Gene Name/Select Gene</p>
  </td>
  <td width=229 style='width:171.75pt;padding:.75pt .75pt .75pt .75pt'>
  <p class=MsoNormal><span class=SpellE>kgXref.geneSymbol</span></p>
  </td>
</tr>
<tr style='mso-yfti-irow:3'>
  <td style='padding:.75pt .75pt .75pt .75pt'>
  <p class=MsoNormal>UCSC ID</p>
  </td>
  <td width=434 style='width:325.25pt;padding:.75pt .75pt .75pt .75pt'>
  <p class=MsoNormal>UCSC Transcript ID</p>
  </td>
  <td width=229 style='width:171.75pt;padding:.75pt .75pt .75pt .75pt'>
  <p class=MsoNormal><span class=SpellE>knownGene.name</span></p>
  </td>
</tr>
<tr style='mso-yfti-irow:4'>
  <td style='padding:.75pt .75pt .75pt .75pt'>
  <p class=MsoNormal><span class=SpellE>UniProtKB</span></p>
  </td>
  <td width=434 style='width:325.25pt;padding:.75pt .75pt .75pt .75pt'>
  <p class=MsoNormal><span class=SpellE>UniProtKB</span> Protein Display ID</p>
  </td>
  <td width=229 style='width:171.75pt;padding:.75pt .75pt .75pt .75pt'>
  <p class=MsoNormal><span class=SpellE>kgXref.spDisplayID</span> or <span
  class=SpellE>kgXref.spID_organism</span></p>
  </td>
</tr>
<tr style='mso-yfti-irow:5'>
  <td style='padding:.75pt .75pt .75pt .75pt'>
  <p class=MsoNormal><span class=SpellE>UniProtKB</span> Acc</p>
  </td>
  <td width=434 style='width:325.25pt;padding:.75pt .75pt .75pt .75pt'>
  <p class=MsoNormal><span class=SpellE>UniProtKB</span> Protein Accession</p>
  </td>
  <td width=229 style='width:171.75pt;padding:.75pt .75pt .75pt .75pt'>
  <p class=MsoNormal><span class=SpellE>kgXref.spID</span></p>
  </td>
</tr>
<tr style='mso-yfti-irow:6'>
  <td style='padding:.75pt .75pt .75pt .75pt'>
  <p class=MsoNormal><span class=SpellE>RefSeq</span></p>
  </td>
  <td width=434 style='width:325.25pt;padding:.75pt .75pt .75pt .75pt'>
  <p class=MsoNormal>NCBI <span class=SpellE>RefSeq</span> Gene Accession</p>
  </td>
  <td width=229 style='width:171.75pt;padding:.75pt .75pt .75pt .75pt'>
  <p class=MsoNormal><span class=SpellE>kgXref.refseq</span></p>
  </td>
</tr>
<tr style='mso-yfti-irow:7'>
  <td style='padding:.75pt .75pt .75pt .75pt'>
  <p class=MsoNormal><span class=SpellE>Entrez</span> Gene</p>
  </td>
  <td width=434 style='width:325.25pt;padding:.75pt .75pt .75pt .75pt'>
  <p class=MsoNormal>NCBI <span class=SpellE>Entrez</span> Gene/<span
  class=SpellE>LocusLink</span> ID</p>
  </td>
  <td width=229 style='width:171.75pt;padding:.75pt .75pt .75pt .75pt'>
  <p class=MsoNormal><span class=SpellE>knownToLocusLink</span></p>
  </td>
</tr>
<tr style='mso-yfti-irow:8'>
  <td style='padding:.75pt .75pt .75pt .75pt'>
  <p class=MsoNormal><span class=SpellE>GenBank</span></p>
  </td>
  <td width=434 style='width:325.25pt;padding:.75pt .75pt .75pt .75pt'>
  <p class=MsoNormal><span class=SpellE>GenBank</span> mRNA Accession</p>
  </td>
  <td width=229 style='width:171.75pt;padding:.75pt .75pt .75pt .75pt'>
  <p class=MsoNormal><span class=SpellE>kgXref.refseq</span> or <span
  class=SpellE>kgXref.mRNA</span></p>
  </td>
</tr>
<tr style='mso-yfti-irow:9'>
  <td style='padding:.75pt .75pt .75pt .75pt'>
  <p class=MsoNormal><span class=SpellE>Ensembl</span></p>
  </td>
  <td width=434 style='width:325.25pt;padding:.75pt .75pt .75pt .75pt'>
  <p class=MsoNormal><span class=SpellE>Ensembl</span> Transcript ID</p>
  </td>
  <td width=229 style='width:171.75pt;padding:.75pt .75pt .75pt .75pt'>
  <p class=MsoNormal><span class=SpellE>knownToEnsembl</span></p>
  </td>
</tr>
<tr style='mso-yfti-irow:10'>
  <td style='padding:.75pt .75pt .75pt .75pt'>
  <p class=MsoNormal>GNF Atlas 2 ID</p>
  </td>
  <td width=434 style='width:325.25pt;padding:.75pt .75pt .75pt .75pt'>
  <p class=MsoNormal>ID of Associated GNF Atlas 2 Expression Data</p>
  </td>
  <td width=229 style='width:171.75pt;padding:.75pt .75pt .75pt .75pt'>
  <p class=MsoNormal>knownToGnfAtlas2</p>
  </td>
</tr>
<tr style='mso-yfti-irow:11'>
  <td style='padding:.75pt .75pt .75pt .75pt'>
  <p class=MsoNormal>Gene Category</p>
  </td>
  <td width=434 style='width:325.25pt;padding:.75pt .75pt .75pt .75pt'>
  <p class=MsoNormal>High Level Gene Category - Coding, Antisense, etc.</p>
  </td>
  <td width=229 style='width:171.75pt;padding:.75pt .75pt .75pt .75pt'>
  <p class=MsoNormal><span class=SpellE>kgTxInfo.category</span></p>
  </td>
</tr>
<tr style='mso-yfti-irow:12'>
  <td style='padding:.75pt .75pt .75pt .75pt'>
  <p class=MsoNormal>CDS Score</p>
  </td>
  <td width=434 style='width:325.25pt;padding:.75pt .75pt .75pt .75pt'>
  <p class=MsoNormal>Coding potential score from <span class=SpellE>txCdsPredict</span></p>
  </td>
  <td width=229 style='width:171.75pt;padding:.75pt .75pt .75pt .75pt'>
  <p class=MsoNormal><span class=SpellE>kgTxInfo.cdsScore</span></p>
  </td>
</tr>
<tr style='mso-yfti-irow:13'>
  <td style='padding:.75pt .75pt .75pt .75pt'>
  <p class=MsoNormal><span class=SpellE>VisiGene</span></p>
  </td>
  <td width=434 style='width:325.25pt;padding:.75pt .75pt .75pt .75pt'>
  <p class=MsoNormal>UCSC <span class=SpellE>VisiGene</span> In Situ Image
  Browser</p>
  </td>
  <td width=229 style='width:171.75pt;padding:.75pt .75pt .75pt .75pt'>
  <p class=MsoNormal><span class=SpellE>knownToVisiGene</span></p>
  </td>
</tr>
<tr style='mso-yfti-irow:14'>
  <td style='padding:.75pt .75pt .75pt .75pt'>
  <p class=MsoNormal>Allen Brain</p>
  </td>
  <td width=434 style='width:325.25pt;padding:.75pt .75pt .75pt .75pt'>
  <p class=MsoNormal>Allen Brain Atlas In Situ Images of Adult Mouse Brains</p>
  </td>
  <td width=229 style='width:171.75pt;padding:.75pt .75pt .75pt .75pt'>
  <p class=MsoNormal><span class=SpellE>knownToAllenBrain</span> &amp; <span
  class=SpellE>allenBrainUrl</span></p>
  </td>
</tr>
<tr style='mso-yfti-irow:15'>
  <td style='padding:.75pt .75pt .75pt .75pt'>
  <p class=MsoNormal>U133 ID</p>
  </td>
  <td width=434 style='width:325.25pt;padding:.75pt .75pt .75pt .75pt'>
  <p class=MsoNormal>ID of Associated <span class=SpellE>Affymetrix</span> U133
  Expression Data </p>
  </td>
  <td width=229 style='width:171.75pt;padding:.75pt .75pt .75pt .75pt'>
  <p class=MsoNormal>knownToU133</p>
  </td>
</tr>
<tr style='mso-yfti-irow:16'>
  <td style='padding:.75pt .75pt .75pt .75pt'>
  <p class=MsoNormal>GNF Atlas 2</p>
  </td>
  <td width=434 style='width:325.25pt;padding:.75pt .75pt .75pt .75pt'>
  <p class=MsoNormal>GNF Expression Atlas 2 Data from U133A and GNF1H Chips</p>
  </td>
  <td width=229 style='width:171.75pt;padding:.75pt .75pt .75pt .75pt'>
  <p class=MsoNormal>gnfAtlas2</p>
  </td>
</tr>
<tr style='mso-yfti-irow:17'>
  <td style='padding:.75pt .75pt .75pt .75pt'>
  <p class=MsoNormal>Max GNF Atlas 2</p>
  </td>
  <td width=434 style='width:325.25pt;padding:.75pt .75pt .75pt .75pt'>
  <p class=MsoNormal>Maximum Expression Value of GNF Expression Atlas 2</p>
  </td>
  <td width=229 style='width:171.75pt;padding:.75pt .75pt .75pt .75pt'>
  <p class=MsoNormal><span class=GramE>calculated</span>?</p>
  </td>
</tr>
<tr style='mso-yfti-irow:18'>
  <td style='padding:.75pt .75pt .75pt .75pt'>
  <p class=MsoNormal>GNF Atlas 2 Delta</p>
  </td>
  <td width=434 style='width:325.25pt;padding:.75pt .75pt .75pt .75pt'>
  <p class=MsoNormal>Normalized Difference in GNF Expression Atlas 2 from
  Selected Gene</p>
  </td>
  <td width=229 style='width:171.75pt;padding:.75pt .75pt .75pt .75pt'>
  <p class=MsoNormal>gnfAtlas2Distance</p>
  </td>
</tr>
<tr style='mso-yfti-irow:19'>
  <td style='padding:.75pt .75pt .75pt .75pt'>
  <p class=MsoNormal>BLASTP<br>
  Bits</p>
  </td>
  <td width=434 style='width:325.25pt;padding:.75pt .75pt .75pt .75pt'>
  <p class=MsoNormal>NCBI BLASTP Bit Score</p>
  </td>
  <td width=229 style='width:171.75pt;padding:.75pt .75pt .75pt .75pt'>
  <p class=MsoNormal><span class=SpellE>knownBlastTab.bitScore</span></p>
  </td>
</tr>
<tr style='mso-yfti-irow:20'>
  <td style='padding:.75pt .75pt .75pt .75pt'>
  <p class=MsoNormal>BLASTP<br>
  E-Value</p>
  </td>
  <td width=434 style='width:325.25pt;padding:.75pt .75pt .75pt .75pt'>
  <p class=MsoNormal>NCBI BLASTP E-Value</p>
  </td>
  <td width=229 style='width:171.75pt;padding:.75pt .75pt .75pt .75pt'>
  <p class=MsoNormal><span class=SpellE>knownBlastTab.evalue</span></p>
  </td>
</tr>
<tr style='mso-yfti-irow:21'>
  <td style='padding:.75pt .75pt .75pt .75pt'>
  <p class=MsoNormal>%ID</p>
  </td>
  <td width=434 style='width:325.25pt;padding:.75pt .75pt .75pt .75pt'>
  <p class=MsoNormal>NCBI BLASTP Percent Identity</p>
  </td>
  <td width=229 style='width:171.75pt;padding:.75pt .75pt .75pt .75pt'>
  <p class=MsoNormal><span class=SpellE>knownBlastTab.identity</span></p>
  </td>
</tr>
<tr style='mso-yfti-irow:22'>
  <td style='padding:.75pt .75pt .75pt .75pt'>
  <p class=MsoNormal>5' UTR Fold</p>
  </td>
  <td width=434 style='width:325.25pt;padding:.75pt .75pt .75pt .75pt'>
  <p class=MsoNormal>5' UTR Fold Energy (Estimated kcal/mol)</p>
  </td>
  <td width=229 style='width:171.75pt;padding:.75pt .75pt .75pt .75pt'>
  <p class=MsoNormal>foldUtr5.energy</p>
  </td>
</tr>
<tr style='mso-yfti-irow:23'>
  <td style='padding:.75pt .75pt .75pt .75pt'>
  <p class=MsoNormal>3' UTR Fold</p>
  </td>
  <td width=434 style='width:325.25pt;padding:.75pt .75pt .75pt .75pt'>
  <p class=MsoNormal>3' UTR Fold Energy (Estimated kcal/mol)</p>
  </td>
  <td width=229 style='width:171.75pt;padding:.75pt .75pt .75pt .75pt'>
  <p class=MsoNormal>foldUtr3.energy</p>
  </td>
</tr>
<tr style='mso-yfti-irow:24'>
  <td style='padding:.75pt .75pt .75pt .75pt'>
  <p class=MsoNormal><span class=SpellE>Exon</span> Count</p>
  </td>
  <td width=434 style='width:325.25pt;padding:.75pt .75pt .75pt .75pt'>
  <p class=MsoNormal>Number of <span class=SpellE>Exons</span> (Including
  Non-Coding)</p>
  </td>
  <td width=229 style='width:171.75pt;padding:.75pt .75pt .75pt .75pt'>
  <p class=MsoNormal><span class=SpellE>knownGene.exonCount</span></p>
  </td>
</tr>
<tr style='mso-yfti-irow:25'>
  <td style='padding:.75pt .75pt .75pt .75pt'>
  <p class=MsoNormal><span class=SpellE>Intron</span> Size</p>
  </td>
  <td width=434 style='width:325.25pt;padding:.75pt .75pt .75pt .75pt'>
  <p class=MsoNormal>Size of biggest (or optionally smallest) <span
  class=SpellE>intron</span></p>
  </td>
  <td width=229 style='width:171.75pt;padding:.75pt .75pt .75pt .75pt'>
  <p class=MsoNormal><span class=SpellE>knownGene</span><span
  style='mso-spacerun:yes'>  </span><span class=SpellE>exonStarts</span> - <span
  class=SpellE>exonEnds</span></p>
  </td>
</tr>
<tr style='mso-yfti-irow:26'>
  <td style='padding:.75pt .75pt .75pt .75pt'>
  <p class=MsoNormal>Genome Position</p>
  </td>
  <td width=434 style='width:325.25pt;padding:.75pt .75pt .75pt .75pt'>
  <p class=MsoNormal>Genome Position/Link to Genome Browser</p>
  </td>
  <td width=229 style='width:171.75pt;padding:.75pt .75pt .75pt .75pt'>
  <p class=MsoNormal>(<span class=SpellE>knownGene.txStart</span> + <span
  class=SpellE>txEnd</span>)/2</p>
  </td>
</tr>
<tr style='mso-yfti-irow:27'>
  <td style='padding:.75pt .75pt .75pt .75pt'>
  <p class=MsoNormal>Mouse</p>
  </td>
  <td width=434 style='width:325.25pt;padding:.75pt .75pt .75pt .75pt'>
  <p class=MsoNormal>Mouse <span class=SpellE>Ortholog</span> (Best <span
  class=SpellE>Blastp</span> Hit to UCSC Known Genes)</p>
  </td>
  <td width=229 style='width:171.75pt;padding:.75pt .75pt .75pt .75pt'>
  <p class=MsoNormal><span class=SpellE>mmBlastTab</span></p>
  </td>
</tr>
<tr style='mso-yfti-irow:28'>
  <td style='padding:.75pt .75pt .75pt .75pt'>
  <p class=MsoNormal>Rat</p>
  </td>
  <td width=434 style='width:325.25pt;padding:.75pt .75pt .75pt .75pt'>
  <p class=MsoNormal>Rat <span class=SpellE>Ortholog</span> (Best <span
  class=SpellE>Blastp</span> Hit to UCSC Known Genes)</p>
  </td>
  <td width=229 style='width:171.75pt;padding:.75pt .75pt .75pt .75pt'>
  <p class=MsoNormal><span class=SpellE>rnBlastTab</span></p>
  </td>
</tr>
<tr style='mso-yfti-irow:29'>
  <td style='padding:.75pt .75pt .75pt .75pt'>
  <p class=MsoNormal><span class=SpellE>Zebrafish</span></p>
  </td>
  <td width=434 style='width:325.25pt;padding:.75pt .75pt .75pt .75pt'>
  <p class=MsoNormal><span class=SpellE><em>Danio</em></span><em> <span
  class=SpellE>rerio</span></em> <span class=SpellE>Ortholog</span> (Best <span
  class=SpellE>Blastp</span> Hit to <span class=SpellE>Ensembl</span>)</p>
  </td>
  <td width=229 style='width:171.75pt;padding:.75pt .75pt .75pt .75pt'>
  <p class=MsoNormal><span class=SpellE>drBlastTab</span></p>
  </td>
</tr>
<tr style='mso-yfti-irow:30'>
  <td style='padding:.75pt .75pt .75pt .75pt'>
  <p class=MsoNormal>Drosophila</p>
  </td>
  <td width=434 style='width:325.25pt;padding:.75pt .75pt .75pt .75pt'>
  <p class=MsoNormal><em>D. <span class=SpellE>melanogaster</span></em> <span
  class=SpellE>Ortholog</span> (Best <span class=SpellE>Blastp</span> Hit to <span
  class=SpellE>FlyBase</span> Proteins)</p>
  </td>
  <td width=229 style='width:171.75pt;padding:.75pt .75pt .75pt .75pt'>
  <p class=MsoNormal><span class=SpellE>dmBlastTab</span></p>
  </td>
</tr>
<tr style='mso-yfti-irow:31'>
  <td style='padding:.75pt .75pt .75pt .75pt'>
  <p class=MsoNormal>C. <span class=SpellE>elegans</span></p>
  </td>
  <td width=434 style='width:325.25pt;padding:.75pt .75pt .75pt .75pt'>
  <p class=MsoNormal><em>C. <span class=SpellE>elegans</span></em> <span
  class=SpellE>Ortholog</span> (Best <span class=SpellE>Blastp</span> Hit to <span
  class=SpellE>WormPep</span>)</p>
  </td>
  <td width=229 style='width:171.75pt;padding:.75pt .75pt .75pt .75pt'>
  <p class=MsoNormal><span class=SpellE>ceBlastTab</span></p>
  </td>
</tr>
<tr style='mso-yfti-irow:32'>
  <td style='padding:.75pt .75pt .75pt .75pt'>
  <p class=MsoNormal>Yeast</p>
  </td>
  <td width=434 style='width:325.25pt;padding:.75pt .75pt .75pt .75pt'>
  <p class=MsoNormal><span class=SpellE><em>Saccharomyces</em></span><em> <span
  class=SpellE>cerevisiae</span></em> <span class=SpellE>Ortholog</span> (Best <span
  class=SpellE>Blastp</span> Hit to <span class=SpellE>RefSeq</span>)</p>
  </td>
  <td width=229 style='width:171.75pt;padding:.75pt .75pt .75pt .75pt'>
  <p class=MsoNormal><span class=SpellE>scBlastTab</span></p>
  </td>
</tr>
<tr style='mso-yfti-irow:33'>
  <td style='padding:.75pt .75pt .75pt .75pt'>
  <p class=MsoNormal><span class=SpellE>Pfam</span> Domains</p>
  </td>
  <td width=434 style='width:325.25pt;padding:.75pt .75pt .75pt .75pt'>
  <p class=MsoNormal>Protein Family Domain Structure</p>
  </td>
  <td width=229 style='width:171.75pt;padding:.75pt .75pt .75pt .75pt'>
  <p class=MsoNormal><span class=SpellE>knownToPfam</span> <span
  style='font-family:Wingdings;mso-ascii-font-family:"Times New Roman";
  mso-hansi-font-family:"Times New Roman";mso-char-type:symbol;mso-symbol-font-family:
  Wingdings'><span style='mso-char-type:symbol;mso-symbol-font-family:Wingdings'>à</span></span>
  <span class=SpellE>pfamDesc</span></p>
  </td>
</tr>
<tr style='mso-yfti-irow:34'>
  <td style='padding:.75pt .75pt .75pt .75pt'>
  <p class=MsoNormal><span class=SpellE>Superfamily</span></p>
  </td>
  <td width=434 style='width:325.25pt;padding:.75pt .75pt .75pt .75pt'>
  <p class=MsoNormal>Protein <span class=SpellE>Superfamily</span> Assignments</p>
  </td>
  <td width=229 style='width:171.75pt;padding:.75pt .75pt .75pt .75pt'>
  <p class=MsoNormal><span class=SpellE>ucscScop</span> &amp; <span
  class=SpellE>scopDesc</span></p>
  </td>
</tr>
<tr style='mso-yfti-irow:35'>
  <td style='padding:.75pt .75pt .75pt .75pt'>
  <p class=MsoNormal>PDB</p>
  </td>
  <td width=434 style='width:325.25pt;padding:.75pt .75pt .75pt .75pt'>
  <p class=MsoNormal>Protein Data Bank</p>
  </td>
  <td width=229 style='width:171.75pt;padding:.75pt .75pt .75pt .75pt'>
  <p class=MsoNormal>kgProtMap2 &amp; sp###### database</p>
  </td>
</tr>
<tr style='mso-yfti-irow:36'>
  <td style='padding:.75pt .75pt .75pt .75pt'>
  <p class=MsoNormal>Gene Ontology</p>
  </td>
  <td width=434 style='width:325.25pt;padding:.75pt .75pt .75pt .75pt'>
  <p class=MsoNormal>Gene Ontology (GO) Terms Associated with Gene</p>
  </td>
  <td width=229 style='width:171.75pt;padding:.75pt .75pt .75pt .75pt'>
  <p class=MsoNormal>kgProtMap2 &amp; sp###### database</p>
  </td>
</tr>
<tr style='mso-yfti-irow:37'>
  <td style='padding:.75pt .75pt .75pt .75pt'>
  <p class=MsoNormal>M. Vidal P2P</p>
  </td>
  <td width=434 style='width:325.25pt;padding:.75pt .75pt .75pt .75pt'>
  <p class=MsoNormal>Human Protein-Protein Interaction Network from Marc Vidal</p>
  </td>
  <td width=229 style='width:171.75pt;padding:.75pt .75pt .75pt .75pt'>
  <p class=MsoNormal>humanVidalP2P</p>
  </td>
</tr>
<tr style='mso-yfti-irow:38'>
  <td style='padding:.75pt .75pt .75pt .75pt'>
  <p class=MsoNormal>E. <span class=SpellE>Wanker</span> P2P</p>
  </td>
  <td width=434 style='width:325.25pt;padding:.75pt .75pt .75pt .75pt'>
  <p class=MsoNormal>Human Protein-Protein Interaction Network from Erich <span
  class=SpellE>Wanker</span></p>
  </td>
  <td width=229 style='width:171.75pt;padding:.75pt .75pt .75pt .75pt'>
  <p class=MsoNormal>humanWankerP2P</p>
  </td>
</tr>
<tr style='mso-yfti-irow:39'>
  <td style='padding:.75pt .75pt .75pt .75pt'>
  <p class=MsoNormal>HPRD P2P</p>
  </td>
  <td width=434 style='width:325.25pt;padding:.75pt .75pt .75pt .75pt'>
  <p class=MsoNormal>Human Protein-Protein Interaction Network from the Human
  Reference Protein Database</p>
  </td>
  <td width=229 style='width:171.75pt;padding:.75pt .75pt .75pt .75pt'>
  <p class=MsoNormal>humanHprdP2P</p>
  </td>
</tr>
<tr style='mso-yfti-irow:40;mso-yfti-lastrow:yes'>
  <td style='padding:.75pt .75pt .75pt .75pt'>
  <p class=MsoNormal>Description</p>
  </td>
  <td width=434 style='width:325.25pt;padding:.75pt .75pt .75pt .75pt'>
  <p class=MsoNormal>Short Description Line/Link to Details Page</p>
  </td>
  <td width=229 style='width:171.75pt;padding:.75pt .75pt .75pt .75pt'>
  <p class=MsoNormal><span class=SpellE>kgXref.description</span></p>
  </td>
</tr>
</table>

Revision as of 23:45, 25 November 2009

File:Hg19uc002ypa.2.pdf

Name

Description

Source

#

Item Number in Displayed List/Select Gene

n/a

Name

Gene Name/Select Gene

kgXref.geneSymbol

UCSC ID

UCSC Transcript ID

knownGene.name

UniProtKB

UniProtKB Protein Display ID

kgXref.spDisplayID or kgXref.spID_organism

UniProtKB Acc

UniProtKB Protein Accession

kgXref.spID

RefSeq

NCBI RefSeq Gene Accession

kgXref.refseq

Entrez Gene

NCBI Entrez Gene/LocusLink ID

knownToLocusLink

GenBank

GenBank mRNA Accession

kgXref.refseq or kgXref.mRNA

Ensembl

Ensembl Transcript ID

knownToEnsembl

GNF Atlas 2 ID

ID of Associated GNF Atlas 2 Expression Data

knownToGnfAtlas2

Gene Category

High Level Gene Category - Coding, Antisense, etc.

kgTxInfo.category

CDS Score

Coding potential score from txCdsPredict

kgTxInfo.cdsScore

VisiGene

UCSC VisiGene In Situ Image Browser

knownToVisiGene

Allen Brain

Allen Brain Atlas In Situ Images of Adult Mouse Brains

knownToAllenBrain & allenBrainUrl

U133 ID

ID of Associated Affymetrix U133 Expression Data

knownToU133

GNF Atlas 2

GNF Expression Atlas 2 Data from U133A and GNF1H Chips

gnfAtlas2

Max GNF Atlas 2

Maximum Expression Value of GNF Expression Atlas 2

calculated?

GNF Atlas 2 Delta

Normalized Difference in GNF Expression Atlas 2 from Selected Gene

gnfAtlas2Distance

BLASTP
Bits

NCBI BLASTP Bit Score

knownBlastTab.bitScore

BLASTP
E-Value

NCBI BLASTP E-Value

knownBlastTab.evalue

%ID

NCBI BLASTP Percent Identity

knownBlastTab.identity

5' UTR Fold

5' UTR Fold Energy (Estimated kcal/mol)

foldUtr5.energy

3' UTR Fold

3' UTR Fold Energy (Estimated kcal/mol)

foldUtr3.energy

Exon Count

Number of Exons (Including Non-Coding)

knownGene.exonCount

Intron Size

Size of biggest (or optionally smallest) intron

knownGene  exonStarts - exonEnds

Genome Position

Genome Position/Link to Genome Browser

(knownGene.txStart + txEnd)/2

Mouse

Mouse Ortholog (Best Blastp Hit to UCSC Known Genes)

mmBlastTab

Rat

Rat Ortholog (Best Blastp Hit to UCSC Known Genes)

rnBlastTab

Zebrafish

Danio rerio Ortholog (Best Blastp Hit to Ensembl)

drBlastTab

Drosophila

D. melanogaster Ortholog (Best Blastp Hit to FlyBase Proteins)

dmBlastTab

C. elegans

C. elegans Ortholog (Best Blastp Hit to WormPep)

ceBlastTab

Yeast

Saccharomyces cerevisiae Ortholog (Best Blastp Hit to RefSeq)

scBlastTab

Pfam Domains

Protein Family Domain Structure

knownToPfam à pfamDesc

Superfamily

Protein Superfamily Assignments

ucscScop & scopDesc

PDB

Protein Data Bank

kgProtMap2 & sp###### database

Gene Ontology

Gene Ontology (GO) Terms Associated with Gene

kgProtMap2 & sp###### database

M. Vidal P2P

Human Protein-Protein Interaction Network from Marc Vidal

humanVidalP2P

E. Wanker P2P

Human Protein-Protein Interaction Network from Erich Wanker

humanWankerP2P

HPRD P2P

Human Protein-Protein Interaction Network from the Human Reference Protein Database

humanHprdP2P

Description

Short Description Line/Link to Details Page

kgXref.description
Retrieved from "https://genomewiki.ucsc.edu/index.php?title=QAing_UCSC_Genes&oldid=8636"