QAing UCSC Genes: Difference between revisions

From genomewiki
Jump to navigationJump to search
(Replacing page with 'This page is no longer maintained.')
 
(27 intermediate revisions by 6 users not shown)
Line 1: Line 1:
== hgGene Page Source Information: ==
This page is no longer maintained.
Click on the following link to view a sample hgGene page annotated with the sources of the different components:
[[Image:hg19uc002ypa.2.pdf|thumb=Image:HgGeneAnnoImage.JPG]] <br>
 
== Gene Sorter Column Sources: ==
 
<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>
 
 
== Table Descriptions ==
Attempt to describe the uses of the tables used in or related to UCSC Genes.
 
=== UCSC Gene and GS Table Descriptions ===
*'''allenBrainGene''' - "Human Cortex Gene Expression" link in "Sequence & Links to Tools & Databases" section of hgGene
*'''allenBrainUrl''' - w/ knownToAllenBrain creates GS column, "Allen Brain"
*'''bioCycMapDesc''' - BioCyc description name in "Biochem & Signaling Pathways" section of hgGene
*'''bioCycPathway''' - BioCyc pathway name in "Biochem & Signaling Pathways" section of hgGene
*'''ccdsKgMap''' - determines the CCDS in the "Other names for this Gene" section of hgGene
*'''ceBlastTab''' - C. elegans info in "Orthologous Genes in Other Species" section of hgGene
*'''cgapAlias''' - links cgapID with kgXref.geneSymbol to pull info for gene
*'''cgapBiocDesc''' -  BioCarta description in "Biochem & Signaling Pathways" section of hgGene
*'''cgapBiocPathway''' - BioCarta pathway name in "Biochem & Signaling Pathways" section of hgGene
*'''dmBlastTab''' - D. melanogaster info in "Orthologous Genes in Other Species" section of hgGene
*'''drBlastTab''' - zebrafish info in "Orthologous Genes in Other Species" section of hgGene
*'''foldUtr3''' - 3' info in "mRNA Secondary Structure of 3' and 5' UTRs" section of hgGene
*'''foldUtr5''' - 5' info in "mRNA Secondary Structure of 3' and 5' UTRs" section of hgGene
*'''gnfAtlas2''' - own track, QA'd with that track, GS, micrary exp data sxn
*'''gnfAtlas2Distance''' - Gene Sorter column "GNF Atlas 2 Delta" & "Expression (GNF Atlas2)" "sort by" option
*'''humanHprdP2P''' - Gene Sorter column "HPRD P2P" & "sort by"
*'''humanVidalP2P''' - Gene Sorter column "M. Vidal Protein-to-Protein" & "sort by"
*'''humanWankerP2P''' - Gene Sorter column "E. Wanker Protein-to-Protein" & "sort by"
*'''keggMapDesc''' - KEGG pathway description in "Biochem & Signaling Pathways" section of hgGene
*'''keggPathway''' - KEGG pathway name in "Biochem & Signaling Pathways" section of hgGene
*'''kg4ToKg5''' - allows searching of an old ID from previous gene set in new gene set or users can check the kg3ToKg4 table directly to find corresponding gene IDs.
*'''kgAlias''' - "Alternate Gene Symbols" in "Other Names for This Gene" section of hgGene
*'''kgColor''' - colors the gene in browser
*'''kgProtAlias''' - intermediate table?
*'''kgProtMap2''' - Scop Domains in "Protein Domain & Structure Information" section of hgGene & Protein Data Bank column in GS need this table to work properly; also involved with proteome browser (not releasing with proteome browser with hg19; being phased out)
*'''kgSpAlias''' - duplicate of kgAlias w/ extra field, spID, that is blank in all records
*'''kgTxInfo''' - provides table info in the "Gene Model Information" section of hgGene
*'''kgXref''' - provides the "Alternate Gene Symbols" in the "Other Names for This Gene" section of hgGene
*'''knownAlt''' - creates a separate track, "Alt Events"; needs to be QA'd separately
*'''knownBlastTab''' - Gene Sorter columns: GS "ID%"=knownBlastTab.identity, GS"BLASTP E-Value"=knownBlastTab.eValue, GS "BLASTP Bits"=knownBlastTab.bitScore)
*'''knownCanonical''' - best transcript from each clusterId (note, GS only works with genes in this table)
*'''knownGene''' - primary table
*'''knownGeneMrna''' - "mRNA" link in "Sequence & Links to Tools &Databases" section of hgGene
*'''knownGenePep''' - "protein" link in "Sequence & Links to Tools &Databases" section of hgGene
*'''knownIsoforms''' - groups transcripts into clusters named by clusterId
*'''knownToAllenBrain''' - w/ allenBrainUrl creates Gene Sorter "Allen Brain" column/link
*'''knownToCdsSnp''' - Dropped because due to too many bugs with table; enabled the Coding SNP column in gene sorter
*'''knownToEnsembl''' - used in link to Ensembl
*'''knownToGnf1h''' - dropped & didn't see changes on hgGene or Gene Sorter, gnfAtlas1?
*'''knownToGnfAtlas2''' - "Microarray..." sxn & Microarray link, GS "GNF Atlas 2 ID"
*'''knownToHprd''' - creates the "HPRD" link in the Seq&lnks to Tls&Dbs section
*'''knownToLocusLink''' - used in link to Entrez Gene, see issues below
*'''knownToPfam''' - gives Pfam Domains section of Prot Dom & Stre info & GS
*'''knownToRefSeq''' - used in link to RefSeq (Other Names)
*'''knownToSuper''' - contains scop domain info with gene name & start/end
*'''knownToTreefam''' - used for link to Treefam website in Seq&lnks to Tls&Dbs
*'''knownToU133''' - Gene Sorter column "U133 ID"
*'''knownToVisiGene''' - used in link to VisiGene
*'''mmBlastTab''' - mouse info in "Orthologous Genes in Other Species" section of hgGene
*'''pfamDesc''' - gives Pfam description in pfam domains section (step in GS)
*'''rnBlastTab''' - rat info in "Orthologous Genes in Other Species" section of hgGene
*'''scBlastTab''' - S. cerevisiae info in "Orthologous Genes in Other Species" section of hgGene
*'''scopDesc''' - prints acc and description in "SCOP Domains" of Prot Dmn * Strtr Info
*'''spMrna''' - intermediate table? Doesn't seem to directly affect hgGene or GS
*'''ucscScop''' - from ucscID gets scop domainName
 
=== Tables Related to UCSC Genes are Separate tracks ===
*affyU133
*allenBrainAli
*exoniphy - created by Adam Siepel of Cornell for each assembly (2nd choice is to lift from previous assembly)
*gnfAtlas2
*nibbImageProbes
*omimGene
*omimGeneMap
*omimMorbidMap
*omimToKnownCanonical
*vgAllProbes
 
=== No longer UCSC Genes Tables ===
*'''knownToCdsSnp''' - dropping on all assemblies. Found too many issues; Populated Cds Snp column in Gene Sorter.
*'''knownToGnf1h''' - part of GNF Atlas 1, which is not on hg19
 
=== Proteome Browser Tables (no longer releasing) ===
*pbAnomLimit
*pbResAvgStd
*pepCCntDist
*pepExonCntDist
*pepHydroDist
*pepIPCntDist
*pepMolWtDist
*pepPi
*pepPiDist
*pepResDist
*pepMwAa

Latest revision as of 19:32, 10 March 2011

This page is no longer maintained.

Retrieved from "https://genomewiki.ucsc.edu/index.php?title=QAing_UCSC_Genes&oldid=13252"