https://wiki.biouml.org/index.php?action=history&feed=atom&title=GTRD_comparison
GTRD comparison - Revision history
2026-04-22T10:56:19Z
Revision history for this page on the wiki
MediaWiki 1.20.3
https://wiki.biouml.org/index.php?title=GTRD_comparison&diff=8435&oldid=prev
Semyonk@dote.ru at 05:45, 8 November 2019
2019-11-08T05:45:26Z
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<tr><td class='diff-marker'> </td><td style="background: #eee; color:black; font-size: smaller;"><div>| Factorbook || total: 1007 <br/> human: 837 || total: 167 <br/> human: 51 || <i>H. sapiens, M. musculus</i> || None || No</div></td><td class='diff-marker'> </td><td style="background: #eee; color:black; font-size: smaller;"><div>| Factorbook || total: 1007 <br/> human: 837 || total: 167 <br/> human: 51 || <i>H. sapiens, M. musculus</i> || None || No</div></td></tr>
<tr><td class='diff-marker'> </td><td style="background: #eee; color:black; font-size: smaller;"><div>|}</div></td><td class='diff-marker'> </td><td style="background: #eee; color:black; font-size: smaller;"><div>|}</div></td></tr>
<tr><td class='diff-marker'>−</td><td style="background: #ffa; color:black; font-size: smaller;"><div><nowiki>*</nowiki>TFs and others (without histone modifications).</div></td><td class='diff-marker'>+</td><td style="background: #cfc; color:black; font-size: smaller;"><div><nowiki>*</nowiki> TFs and others (without histone modifications).</div></td></tr>
<tr><td class='diff-marker'>−</td><td style="background: #ffa; color:black; font-size: smaller;"><div><br/><nowiki>**</nowiki>The number of ChIP-seq samples cannot be directly compared between databases as definition of sample may be distinct.</div></td><td class='diff-marker'>+</td><td style="background: #cfc; color:black; font-size: smaller;"><div><br/><nowiki>**</nowiki> The number of ChIP-seq samples cannot be directly compared between databases as definition of sample may be distinct.</div></td></tr>
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Semyonk@dote.ru
https://wiki.biouml.org/index.php?title=GTRD_comparison&diff=8434&oldid=prev
Semyonk@dote.ru at 05:45, 8 November 2019
2019-11-08T05:45:11Z
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<td colspan='2' style="background-color: white; color:black;">Revision as of 05:45, 8 November 2019</td>
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<tr><td class='diff-marker'> </td><td style="background: #eee; color:black; font-size: smaller;"><div><nowiki>*</nowiki>TFs and others (without histone modifications).</div></td><td class='diff-marker'> </td><td style="background: #eee; color:black; font-size: smaller;"><div><nowiki>*</nowiki>TFs and others (without histone modifications).</div></td></tr>
<tr><td class='diff-marker'>−</td><td style="background: #ffa; color:black; font-size: smaller;"><div><nowiki>**</nowiki>The number of ChIP-seq samples cannot be directly compared between databases as definition of sample may be distinct.</div></td><td class='diff-marker'>+</td><td style="background: #cfc; color:black; font-size: smaller;"><div><ins class="diffchange diffchange-inline"><br/></ins><nowiki>**</nowiki>The number of ChIP-seq samples cannot be directly compared between databases as definition of sample may be distinct.</div></td></tr>
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Semyonk@dote.ru
https://wiki.biouml.org/index.php?title=GTRD_comparison&diff=8433&oldid=prev
Semyonk@dote.ru at 05:44, 8 November 2019
2019-11-08T05:44:55Z
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<tr><td class='diff-marker'> </td><td style="background: #eee; color:black; font-size: smaller;"><div>{| class="wikitable"</div></td><td class='diff-marker'> </td><td style="background: #eee; color:black; font-size: smaller;"><div>{| class="wikitable"</div></td></tr>
<tr><td class='diff-marker'>−</td><td style="background: #ffa; color:black; font-size: smaller;"><div>! Database !! Number of TF <del class="diffchange diffchange-inline">( * - and others ) </del>ChIP-seq samples <br/><del class="diffchange diffchange-inline">(** - with input controls)</del>!! Number of <del class="diffchange diffchange-inline">TF ( * - and others ) </del>!! Species !! ChIP-seq peak callers !! Metacluster approach</div></td><td class='diff-marker'>+</td><td style="background: #cfc; color:black; font-size: smaller;"><div>! Database !! Number of TF ChIP-seq samples <br/>!! Number of <ins class="diffchange diffchange-inline">TFs </ins>!! Species !! ChIP-seq peak callers !! Metacluster approach</div></td></tr>
<tr><td class='diff-marker'> </td><td style="background: #eee; color:black; font-size: smaller;"><div>|-</div></td><td class='diff-marker'> </td><td style="background: #eee; color:black; font-size: smaller;"><div>|-</div></td></tr>
<tr><td class='diff-marker'>−</td><td style="background: #ffa; color:black; font-size: smaller;"><div>| GTRD v19.10 || total: <del class="diffchange diffchange-inline">20979</del>* <br/> human: <del class="diffchange diffchange-inline">9760</del>* || total: 3376* <br/> human: 1339* || <i>H. sapiens, M. musculus, R. norvegicus, <br/> D. melanogaster, C. elegans, D. rerio, <br/> S. pombe, S. cerevisiae, A. thaliana</i> || MACS2, SISSRs, GEM, PICS || Yes   </div></td><td class='diff-marker'>+</td><td style="background: #cfc; color:black; font-size: smaller;"><div>| GTRD v19.10 || total: <ins class="diffchange diffchange-inline">30670</ins>* <br/> human: <ins class="diffchange diffchange-inline">13515</ins>* || total: 3376* <br/> human: 1339* || <i>H. sapiens, M. musculus, R. norvegicus, <br/> D. melanogaster, C. elegans, D. rerio, <br/> S. pombe, S. cerevisiae, A. thaliana</i> || MACS2, SISSRs, GEM, PICS || Yes   </div></td></tr>
<tr><td class='diff-marker'> </td><td style="background: #eee; color:black; font-size: smaller;"><div>|-</div></td><td class='diff-marker'> </td><td style="background: #eee; color:black; font-size: smaller;"><div>|-</div></td></tr>
<tr><td class='diff-marker'> </td><td style="background: #eee; color:black; font-size: smaller;"><div>| ChIP-Atlas || total: 22872* <br/> human: 10129* || total: 1972* <br/> human: 878* || <i>H. sapiens, M. musculus, R. norvegicus, <br/> D. melanogaster, C. elegans, S. cerevisiae</i> || MACS2 || No</div></td><td class='diff-marker'> </td><td style="background: #eee; color:black; font-size: smaller;"><div>| ChIP-Atlas || total: 22872* <br/> human: 10129* || total: 1972* <br/> human: 878* || <i>H. sapiens, M. musculus, R. norvegicus, <br/> D. melanogaster, C. elegans, S. cerevisiae</i> || MACS2 || No</div></td></tr>
<tr><td class='diff-marker'> </td><td style="background: #eee; color:black; font-size: smaller;"><div>|-</div></td><td class='diff-marker'> </td><td style="background: #eee; color:black; font-size: smaller;"><div>|-</div></td></tr>
<tr><td class='diff-marker'>−</td><td style="background: #ffa; color:black; font-size: smaller;"><div>| Cistrome DB || total: 24065<del class="diffchange diffchange-inline">* *</del>* <br/> human: 13976<del class="diffchange diffchange-inline">* *</del>* || total: Unknown <br/>  human: Unknown || <i>H. sapiens, M. musculus</i> || MACS2 || No</div></td><td class='diff-marker'>+</td><td style="background: #cfc; color:black; font-size: smaller;"><div>| Cistrome DB || total: 24065* <br/> human: 13976* || total: Unknown <br/>  human: Unknown || <i>H. sapiens, M. musculus</i> || MACS2 || No</div></td></tr>
<tr><td class='diff-marker'> </td><td style="background: #eee; color:black; font-size: smaller;"><div>|-</div></td><td class='diff-marker'> </td><td style="background: #eee; color:black; font-size: smaller;"><div>|-</div></td></tr>
<tr><td class='diff-marker'> </td><td style="background: #eee; color:black; font-size: smaller;"><div>| NGS-QC || total: 22398* <br/> human: 11597* || total: Unkonwn <br/> human: Unknown || <i>H. sapiens, M. musculus, R. norvegicus, <br/> D. rerio, C. elegans, D. melanogaster, <br/> S. cerevisiae, A. thaliana, G. gallus, <br/> P. troglodytes</i> || None || No</div></td><td class='diff-marker'> </td><td style="background: #eee; color:black; font-size: smaller;"><div>| NGS-QC || total: 22398* <br/> human: 11597* || total: Unkonwn <br/> human: Unknown || <i>H. sapiens, M. musculus, R. norvegicus, <br/> D. rerio, C. elegans, D. melanogaster, <br/> S. cerevisiae, A. thaliana, G. gallus, <br/> P. troglodytes</i> || None || No</div></td></tr>
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<tr><td class='diff-marker'> </td><td style="background: #eee; color:black; font-size: smaller;"><div>| Factorbook || total: 1007 <br/> human: 837 || total: 167 <br/> human: 51 || <i>H. sapiens, M. musculus</i> || None || No</div></td><td class='diff-marker'> </td><td style="background: #eee; color:black; font-size: smaller;"><div>| Factorbook || total: 1007 <br/> human: 837 || total: 167 <br/> human: 51 || <i>H. sapiens, M. musculus</i> || None || No</div></td></tr>
<tr><td class='diff-marker'> </td><td style="background: #eee; color:black; font-size: smaller;"><div>|}</div></td><td class='diff-marker'> </td><td style="background: #eee; color:black; font-size: smaller;"><div>|}</div></td></tr>
<tr><td class='diff-marker'>−</td><td style="background: #ffa; color:black; font-size: smaller;"><div> </div></td><td class='diff-marker'>+</td><td style="background: #cfc; color:black; font-size: smaller;"><div><nowiki>*<ins class="diffchange diffchange-inline"></nowiki>TFs and others (without histone modifications).</ins></div></td></tr>
<tr><td class='diff-marker'>−</td><td style="background: #ffa; color:black; font-size: smaller;"><div><nowiki>***</nowiki>The number of ChIP-seq samples cannot be directly compared between databases as definition of sample may be distinct.</div></td><td class='diff-marker'>+</td><td style="background: #cfc; color:black; font-size: smaller;"><div><ins class="diffchange diffchange-inline"><nowiki></ins>**</nowiki>The number of ChIP-seq samples cannot be directly compared between databases as definition of sample may be distinct.</div></td></tr>
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Semyonk@dote.ru
https://wiki.biouml.org/index.php?title=GTRD_comparison&diff=8431&oldid=prev
Semyonk@dote.ru at 05:09, 8 November 2019
2019-11-08T05:09:12Z
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<td colspan='2' style="background-color: white; color:black;">Revision as of 05:09, 8 November 2019</td>
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<tr><td class='diff-marker'> </td><td style="background: #eee; color:black; font-size: smaller;"><div>{| class="wikitable"</div></td><td class='diff-marker'> </td><td style="background: #eee; color:black; font-size: smaller;"><div>{| class="wikitable"</div></td></tr>
<tr><td class='diff-marker'>−</td><td style="background: #ffa; color:black; font-size: smaller;"><div>! Database !! Number of TF ( * - and others ) ChIP-seq samples (<del class="diffchange diffchange-inline">without </del>input controls)!! Number of TF ( * - and others ) !! Species !! ChIP-seq peak callers !! Metacluster approach</div></td><td class='diff-marker'>+</td><td style="background: #cfc; color:black; font-size: smaller;"><div>! Database !! Number of TF ( * - and others ) ChIP-seq samples <ins class="diffchange diffchange-inline"><br/></ins>(<ins class="diffchange diffchange-inline">** - with </ins>input controls)!! Number of TF ( * - and others ) !! Species !! ChIP-seq peak callers !! Metacluster approach</div></td></tr>
<tr><td class='diff-marker'> </td><td style="background: #eee; color:black; font-size: smaller;"><div>|-</div></td><td class='diff-marker'> </td><td style="background: #eee; color:black; font-size: smaller;"><div>|-</div></td></tr>
<tr><td class='diff-marker'> </td><td style="background: #eee; color:black; font-size: smaller;"><div>| GTRD v19.10 || total: 20979* <br/> human: 9760* || total: 3376* <br/> human: 1339* || <i>H. sapiens, M. musculus, R. norvegicus, <br/> D. melanogaster, C. elegans, D. rerio, <br/> S. pombe, S. cerevisiae, A. thaliana</i> || MACS2, SISSRs, GEM, PICS || Yes   </div></td><td class='diff-marker'> </td><td style="background: #eee; color:black; font-size: smaller;"><div>| GTRD v19.10 || total: 20979* <br/> human: 9760* || total: 3376* <br/> human: 1339* || <i>H. sapiens, M. musculus, R. norvegicus, <br/> D. melanogaster, C. elegans, D. rerio, <br/> S. pombe, S. cerevisiae, A. thaliana</i> || MACS2, SISSRs, GEM, PICS || Yes   </div></td></tr>
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<tr><td class='diff-marker'> </td><td style="background: #eee; color:black; font-size: smaller;"><div>| ChIP-Atlas || total: 22872* <br/> human: 10129* || total: 1972* <br/> human: 878* || <i>H. sapiens, M. musculus, R. norvegicus, <br/> D. melanogaster, C. elegans, S. cerevisiae</i> || MACS2 || No</div></td><td class='diff-marker'> </td><td style="background: #eee; color:black; font-size: smaller;"><div>| ChIP-Atlas || total: 22872* <br/> human: 10129* || total: 1972* <br/> human: 878* || <i>H. sapiens, M. musculus, R. norvegicus, <br/> D. melanogaster, C. elegans, S. cerevisiae</i> || MACS2 || No</div></td></tr>
<tr><td class='diff-marker'> </td><td style="background: #eee; color:black; font-size: smaller;"><div>|-</div></td><td class='diff-marker'> </td><td style="background: #eee; color:black; font-size: smaller;"><div>|-</div></td></tr>
<tr><td class='diff-marker'>−</td><td style="background: #ffa; color:black; font-size: smaller;"><div>| Cistrome DB || total: 24065* <br/> human: 13976* || total: Unknown <br/>  human: Unknown || <i>H. sapiens, M. musculus</i> || MACS2 || No</div></td><td class='diff-marker'>+</td><td style="background: #cfc; color:black; font-size: smaller;"><div>| Cistrome DB || total: 24065<ins class="diffchange diffchange-inline">* *</ins>* <br/> human: 13976<ins class="diffchange diffchange-inline">* *</ins>* || total: Unknown <br/>  human: Unknown || <i>H. sapiens, M. musculus</i> || MACS2 || No</div></td></tr>
<tr><td class='diff-marker'> </td><td style="background: #eee; color:black; font-size: smaller;"><div>|-</div></td><td class='diff-marker'> </td><td style="background: #eee; color:black; font-size: smaller;"><div>|-</div></td></tr>
<tr><td class='diff-marker'>−</td><td style="background: #ffa; color:black; font-size: smaller;"><div>| NGS-QC || total: 22398 <br/> human: 11597 || total: Unkonwn <br/> human: Unknown || <i>H. sapiens, M. musculus, R. norvegicus, <br/> D. rerio, C. elegans, D. melanogaster, <br/> S. cerevisiae, A. thaliana, G. gallus, <br/> P. troglodytes</i> || None || No</div></td><td class='diff-marker'>+</td><td style="background: #cfc; color:black; font-size: smaller;"><div>| NGS-QC || total: 22398<ins class="diffchange diffchange-inline">* </ins><br/> human: 11597<ins class="diffchange diffchange-inline">* </ins>|| total: Unkonwn <br/> human: Unknown || <i>H. sapiens, M. musculus, R. norvegicus, <br/> D. rerio, C. elegans, D. melanogaster, <br/> S. cerevisiae, A. thaliana, G. gallus, <br/> P. troglodytes</i> || None || No</div></td></tr>
<tr><td class='diff-marker'> </td><td style="background: #eee; color:black; font-size: smaller;"><div>|-</div></td><td class='diff-marker'> </td><td style="background: #eee; color:black; font-size: smaller;"><div>|-</div></td></tr>
<tr><td class='diff-marker'>−</td><td style="background: #ffa; color:black; font-size: smaller;"><div>| ENCODE || total: 3609 <br/> human: 2407 || total: Unknown <br/> human: Unknown || <i>H. sapiens, M. musculus, D. melanogaster, <br/> C. elegans</i> || SPP || No</div></td><td class='diff-marker'>+</td><td style="background: #cfc; color:black; font-size: smaller;"><div>| ENCODE || total: 3609<ins class="diffchange diffchange-inline">* </ins><br/> human: 2407 || total: Unknown <br/> human: Unknown || <i>H. sapiens, M. musculus, D. melanogaster, <br/> C. elegans</i> || SPP || No</div></td></tr>
<tr><td class='diff-marker'> </td><td style="background: #eee; color:black; font-size: smaller;"><div>|-</div></td><td class='diff-marker'> </td><td style="background: #eee; color:black; font-size: smaller;"><div>|-</div></td></tr>
<tr><td class='diff-marker'> </td><td style="background: #eee; color:black; font-size: smaller;"><div>| ChIPBase || total: 4300 <br/> human: 2498 || total: 870 <br/> human: Unknown || <i>H. sapiens, M. musculus, R. norvegicus, <br/> D. rerio, X. tropicalis, C. elegans, <br/> D. melanogaster, S. cerevisiae, A. thaliana, <br/> G. gallus</i> || >10 in total, but no uniform pipeline, <br/> each ChIP-seq is processed by different peak caller  || No</div></td><td class='diff-marker'> </td><td style="background: #eee; color:black; font-size: smaller;"><div>| ChIPBase || total: 4300 <br/> human: 2498 || total: 870 <br/> human: Unknown || <i>H. sapiens, M. musculus, R. norvegicus, <br/> D. rerio, X. tropicalis, C. elegans, <br/> D. melanogaster, S. cerevisiae, A. thaliana, <br/> G. gallus</i> || >10 in total, but no uniform pipeline, <br/> each ChIP-seq is processed by different peak caller  || No</div></td></tr>
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<tr><td class='diff-marker'> </td><td style="background: #eee; color:black; font-size: smaller;"></td><td class='diff-marker'> </td><td style="background: #eee; color:black; font-size: smaller;"></td></tr>
<tr><td class='diff-marker'>−</td><td style="background: #ffa; color:black; font-size: smaller;"><div><nowiki>**</nowiki>The number of ChIP-seq samples cannot be directly compared between databases as definition of sample may be distinct.</div></td><td class='diff-marker'>+</td><td style="background: #cfc; color:black; font-size: smaller;"><div><nowiki><ins class="diffchange diffchange-inline">*</ins>**</nowiki>The number of ChIP-seq samples cannot be directly compared between databases as definition of sample may be distinct.</div></td></tr>
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Semyonk@dote.ru
https://wiki.biouml.org/index.php?title=GTRD_comparison&diff=8428&oldid=prev
Semyonk@dote.ru at 05:02, 8 November 2019
2019-11-08T05:02:31Z
<p></p>
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<td colspan='2' style="background-color: white; color:black;">Revision as of 05:02, 8 November 2019</td>
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<tr><td class='diff-marker'> </td><td style="background: #eee; color:black; font-size: smaller;"><div>| Cistrome DB || total: 24065* <br/> human: 13976* || total: Unknown <br/>  human: Unknown || <i>H. sapiens, M. musculus</i> || MACS2 || No</div></td><td class='diff-marker'> </td><td style="background: #eee; color:black; font-size: smaller;"><div>| Cistrome DB || total: 24065* <br/> human: 13976* || total: Unknown <br/>  human: Unknown || <i>H. sapiens, M. musculus</i> || MACS2 || No</div></td></tr>
<tr><td class='diff-marker'> </td><td style="background: #eee; color:black; font-size: smaller;"><div>|-</div></td><td class='diff-marker'> </td><td style="background: #eee; color:black; font-size: smaller;"><div>|-</div></td></tr>
<tr><td class='diff-marker'>−</td><td style="background: #ffa; color:black; font-size: smaller;"><div>| <del class="diffchange diffchange-inline">ReMap 2018 v1.2 </del>|| total: <del class="diffchange diffchange-inline">2829* </del><br/> human: <del class="diffchange diffchange-inline">2829* </del>|| total: <del class="diffchange diffchange-inline">485 </del><br/> human: <del class="diffchange diffchange-inline">485 </del>|| <i>H. sapiens</i> || <del class="diffchange diffchange-inline">MACS2 </del>|| <del class="diffchange diffchange-inline">Yes (CRMs)</del></div></td><td class='diff-marker'>+</td><td style="background: #cfc; color:black; font-size: smaller;"><div>| <ins class="diffchange diffchange-inline">NGS-QC </ins>|| total: <ins class="diffchange diffchange-inline">22398 </ins><br/> human: <ins class="diffchange diffchange-inline">11597 </ins>|| total: <ins class="diffchange diffchange-inline">Unkonwn </ins><br/> human: <ins class="diffchange diffchange-inline">Unknown </ins>|| <i>H. sapiens<ins class="diffchange diffchange-inline">, M. musculus, R. norvegicus, <br/> D. rerio, C. elegans, D. melanogaster, <br/> S. cerevisiae, A. thaliana, G. gallus, <br/> P. troglodytes</ins></i> || <ins class="diffchange diffchange-inline">None </ins>|| <ins class="diffchange diffchange-inline">No</ins></div></td></tr>
<tr><td class='diff-marker'> </td><td style="background: #eee; color:black; font-size: smaller;"><div>|-</div></td><td class='diff-marker'> </td><td style="background: #eee; color:black; font-size: smaller;"><div>|-</div></td></tr>
<tr><td class='diff-marker'> </td><td style="background: #eee; color:black; font-size: smaller;"><div>| ENCODE || total: 3609 <br/> human: 2407 || total: Unknown <br/> human: Unknown || <i>H. sapiens, M. musculus, D. melanogaster, <br/> C. elegans</i> || SPP || No</div></td><td class='diff-marker'> </td><td style="background: #eee; color:black; font-size: smaller;"><div>| ENCODE || total: 3609 <br/> human: 2407 || total: Unknown <br/> human: Unknown || <i>H. sapiens, M. musculus, D. melanogaster, <br/> C. elegans</i> || SPP || No</div></td></tr>
<tr><td colspan="2" class="diff-lineno">Line 14:</td>
<td colspan="2" class="diff-lineno">Line 14:</td></tr>
<tr><td class='diff-marker'> </td><td style="background: #eee; color:black; font-size: smaller;"><div>| ChIPBase || total: 4300 <br/> human: 2498 || total: 870 <br/> human: Unknown || <i>H. sapiens, M. musculus, R. norvegicus, <br/> D. rerio, X. tropicalis, C. elegans, <br/> D. melanogaster, S. cerevisiae, A. thaliana, <br/> G. gallus</i> || >10 in total, but no uniform pipeline, <br/> each ChIP-seq is processed by different peak caller  || No</div></td><td class='diff-marker'> </td><td style="background: #eee; color:black; font-size: smaller;"><div>| ChIPBase || total: 4300 <br/> human: 2498 || total: 870 <br/> human: Unknown || <i>H. sapiens, M. musculus, R. norvegicus, <br/> D. rerio, X. tropicalis, C. elegans, <br/> D. melanogaster, S. cerevisiae, A. thaliana, <br/> G. gallus</i> || >10 in total, but no uniform pipeline, <br/> each ChIP-seq is processed by different peak caller  || No</div></td></tr>
<tr><td class='diff-marker'> </td><td style="background: #eee; color:black; font-size: smaller;"><div>|-</div></td><td class='diff-marker'> </td><td style="background: #eee; color:black; font-size: smaller;"><div>|-</div></td></tr>
<tr><td class='diff-marker'>−</td><td style="background: #ffa; color:black; font-size: smaller;"><div>| <del class="diffchange diffchange-inline">Factorbook </del>|| total: <del class="diffchange diffchange-inline">1007 </del><br/> human: <del class="diffchange diffchange-inline">837 </del>|| total: <del class="diffchange diffchange-inline">167 </del><br/> human: <del class="diffchange diffchange-inline">51 </del>|| <i>H. sapiens<del class="diffchange diffchange-inline">, M. musculus</del></i> || <del class="diffchange diffchange-inline">None </del>|| <del class="diffchange diffchange-inline">No</del></div></td><td class='diff-marker'>+</td><td style="background: #cfc; color:black; font-size: smaller;"><div>| <ins class="diffchange diffchange-inline">ReMap 2018 v1.2 </ins>|| total: <ins class="diffchange diffchange-inline">2829* </ins><br/> human: <ins class="diffchange diffchange-inline">2829* </ins>|| total: <ins class="diffchange diffchange-inline">485 </ins><br/> human: <ins class="diffchange diffchange-inline">485 </ins>|| <i>H. sapiens</i> || <ins class="diffchange diffchange-inline">MACS2 </ins>|| <ins class="diffchange diffchange-inline">Yes (CRMs)</ins></div></td></tr>
<tr><td class='diff-marker'> </td><td style="background: #eee; color:black; font-size: smaller;"><div>|-</div></td><td class='diff-marker'> </td><td style="background: #eee; color:black; font-size: smaller;"><div>|-</div></td></tr>
<tr><td class='diff-marker'>−</td><td style="background: #ffa; color:black; font-size: smaller;"><div>| <del class="diffchange diffchange-inline">NGS-QC </del>|| total: <del class="diffchange diffchange-inline">22398 </del><br/> human: <del class="diffchange diffchange-inline">11597 </del>|| total: <del class="diffchange diffchange-inline">Unkonwn </del><br/> human: <del class="diffchange diffchange-inline">Unknown </del>|| <i>H. sapiens, M. musculus<del class="diffchange diffchange-inline">, R. norvegicus, <br/> D. rerio, C. elegans, D. melanogaster, <br/> S. cerevisiae, A. thaliana, G. gallus, <br/> P. troglodytes</del></i> || None || No</div></td><td class='diff-marker'>+</td><td style="background: #cfc; color:black; font-size: smaller;"><div>| <ins class="diffchange diffchange-inline">Factorbook </ins>|| total: <ins class="diffchange diffchange-inline">1007 </ins><br/> human: <ins class="diffchange diffchange-inline">837 </ins>|| total: <ins class="diffchange diffchange-inline">167 </ins><br/> human: <ins class="diffchange diffchange-inline">51 </ins>|| <i>H. sapiens, M. musculus</i> || None || No</div></td></tr>
<tr><td class='diff-marker'> </td><td style="background: #eee; color:black; font-size: smaller;"><div>|}</div></td><td class='diff-marker'> </td><td style="background: #eee; color:black; font-size: smaller;"><div>|}</div></td></tr>
<tr><td class='diff-marker'> </td><td style="background: #eee; color:black; font-size: smaller;"></td><td class='diff-marker'> </td><td style="background: #eee; color:black; font-size: smaller;"></td></tr>
<tr><td class='diff-marker'> </td><td style="background: #eee; color:black; font-size: smaller;"><div><nowiki>**</nowiki>The number of ChIP-seq samples cannot be directly compared between databases as definition of sample may be distinct.</div></td><td class='diff-marker'> </td><td style="background: #eee; color:black; font-size: smaller;"><div><nowiki>**</nowiki>The number of ChIP-seq samples cannot be directly compared between databases as definition of sample may be distinct.</div></td></tr>
</table>
Semyonk@dote.ru
https://wiki.biouml.org/index.php?title=GTRD_comparison&diff=8427&oldid=prev
Semyonk@dote.ru at 05:00, 8 November 2019
2019-11-08T05:00:37Z
<p></p>
<table class='diff diff-contentalign-left'>
<col class='diff-marker' />
<col class='diff-content' />
<col class='diff-marker' />
<col class='diff-content' />
<tr style='vertical-align: top;'>
<td colspan='2' style="background-color: white; color:black;">← Older revision</td>
<td colspan='2' style="background-color: white; color:black;">Revision as of 05:00, 8 November 2019</td>
</tr><tr><td colspan="2" class="diff-lineno">Line 1:</td>
<td colspan="2" class="diff-lineno">Line 1:</td></tr>
<tr><td class='diff-marker'> </td><td style="background: #eee; color:black; font-size: smaller;"><div>{| class="wikitable"</div></td><td class='diff-marker'> </td><td style="background: #eee; color:black; font-size: smaller;"><div>{| class="wikitable"</div></td></tr>
<tr><td class='diff-marker'>−</td><td style="background: #ffa; color:black; font-size: smaller;"><div>! Database !! Number of TF ChIP-seq samples !! Number of TF ( * - and others ) !! Species !! ChIP-seq peak callers !! Metacluster approach</div></td><td class='diff-marker'>+</td><td style="background: #cfc; color:black; font-size: smaller;"><div>! Database !! Number of TF <ins class="diffchange diffchange-inline">( * - and others ) </ins>ChIP-seq samples <ins class="diffchange diffchange-inline">(without input controls)</ins>!! Number of TF ( * - and others ) !! Species !! ChIP-seq peak callers !! Metacluster approach</div></td></tr>
<tr><td class='diff-marker'> </td><td style="background: #eee; color:black; font-size: smaller;"><div>|-</div></td><td class='diff-marker'> </td><td style="background: #eee; color:black; font-size: smaller;"><div>|-</div></td></tr>
<tr><td class='diff-marker'>−</td><td style="background: #ffa; color:black; font-size: smaller;"><div>| GTRD v19.10 || total: <del class="diffchange diffchange-inline">30670 </del><br/> human: <del class="diffchange diffchange-inline">13515 </del>|| total: 3376 <br/> human: 1339 || <i>H. sapiens, M. musculus, R. norvegicus, <br/> D. melanogaster, C. elegans, D. rerio, <br/> S. pombe, S. cerevisiae, A. thaliana</i> || MACS2, SISSRs, GEM, PICS || Yes   </div></td><td class='diff-marker'>+</td><td style="background: #cfc; color:black; font-size: smaller;"><div>| GTRD v19.10 || total: <ins class="diffchange diffchange-inline">20979* </ins><br/> human: <ins class="diffchange diffchange-inline">9760* </ins>|| total: 3376<ins class="diffchange diffchange-inline">* </ins><br/> human: 1339<ins class="diffchange diffchange-inline">* </ins>|| <i>H. sapiens, M. musculus, R. norvegicus, <br/> D. melanogaster, C. elegans, D. rerio, <br/> S. pombe, S. cerevisiae, A. thaliana</i> || MACS2, SISSRs, GEM, PICS || Yes   </div></td></tr>
<tr><td class='diff-marker'> </td><td style="background: #eee; color:black; font-size: smaller;"><div>|-</div></td><td class='diff-marker'> </td><td style="background: #eee; color:black; font-size: smaller;"><div>|-</div></td></tr>
<tr><td class='diff-marker'>−</td><td style="background: #ffa; color:black; font-size: smaller;"><div>| ChIP-Atlas || total: <del class="diffchange diffchange-inline">19414</del>* <br/> human: <del class="diffchange diffchange-inline">8368</del>* || total: <del class="diffchange diffchange-inline">1929 </del><br/> human: <del class="diffchange diffchange-inline">820 </del>|| <i>H. sapiens, M. musculus, R. norvegicus, <br/> D. melanogaster, C. elegans, S. cerevisiae</i> || MACS2 || No</div></td><td class='diff-marker'>+</td><td style="background: #cfc; color:black; font-size: smaller;"><div>| ChIP-Atlas || total: <ins class="diffchange diffchange-inline">22872</ins>* <br/> human: <ins class="diffchange diffchange-inline">10129</ins>* || total: <ins class="diffchange diffchange-inline">1972* </ins><br/> human: <ins class="diffchange diffchange-inline">878* </ins>|| <i>H. sapiens, M. musculus, R. norvegicus, <br/> D. melanogaster, C. elegans, S. cerevisiae</i> || MACS2 || No</div></td></tr>
<tr><td class='diff-marker'> </td><td style="background: #eee; color:black; font-size: smaller;"><div>|-</div></td><td class='diff-marker'> </td><td style="background: #eee; color:black; font-size: smaller;"><div>|-</div></td></tr>
<tr><td class='diff-marker'>−</td><td style="background: #ffa; color:black; font-size: smaller;"><div>| Cistrome DB || total: <del class="diffchange diffchange-inline">20408</del>* <br/> human: <del class="diffchange diffchange-inline">11348</del>* || total: Unknown <br/>  human: Unknown || <i>H. sapiens, M. musculus</i> || MACS2 || No</div></td><td class='diff-marker'>+</td><td style="background: #cfc; color:black; font-size: smaller;"><div>| Cistrome DB || total: <ins class="diffchange diffchange-inline">24065</ins>* <br/> human: <ins class="diffchange diffchange-inline">13976</ins>* || total: Unknown <br/>  human: Unknown || <i>H. sapiens, M. musculus</i> || MACS2 || No</div></td></tr>
<tr><td class='diff-marker'> </td><td style="background: #eee; color:black; font-size: smaller;"><div>|-</div></td><td class='diff-marker'> </td><td style="background: #eee; color:black; font-size: smaller;"><div>|-</div></td></tr>
<tr><td class='diff-marker'>−</td><td style="background: #ffa; color:black; font-size: smaller;"><div>| ReMap 2018 || total: 2829* <br/> human: 2829* || total: 485 <br/> human: 485 || <i>H. sapiens</i> || MACS2 || Yes (CRMs)</div></td><td class='diff-marker'>+</td><td style="background: #cfc; color:black; font-size: smaller;"><div>| ReMap 2018 <ins class="diffchange diffchange-inline">v1.2 </ins>|| total: 2829* <br/> human: 2829* || total: 485 <br/> human: 485 || <i>H. sapiens</i> || MACS2 || Yes (CRMs)</div></td></tr>
<tr><td class='diff-marker'> </td><td style="background: #eee; color:black; font-size: smaller;"><div>|-</div></td><td class='diff-marker'> </td><td style="background: #eee; color:black; font-size: smaller;"><div>|-</div></td></tr>
<tr><td class='diff-marker'>−</td><td style="background: #ffa; color:black; font-size: smaller;"><div>| ENCODE || total: <del class="diffchange diffchange-inline">3684 </del><br/> human: <del class="diffchange diffchange-inline">2489 </del>|| total: Unknown <br/> human: Unknown || <i>H. sapiens, M. musculus, D. melanogaster, <br/> C. elegans</i> || SPP || No</div></td><td class='diff-marker'>+</td><td style="background: #cfc; color:black; font-size: smaller;"><div>| ENCODE || total: <ins class="diffchange diffchange-inline">3609 </ins><br/> human: <ins class="diffchange diffchange-inline">2407 </ins>|| total: Unknown <br/> human: Unknown || <i>H. sapiens, M. musculus, D. melanogaster, <br/> C. elegans</i> || SPP || No</div></td></tr>
<tr><td class='diff-marker'> </td><td style="background: #eee; color:black; font-size: smaller;"><div>|-</div></td><td class='diff-marker'> </td><td style="background: #eee; color:black; font-size: smaller;"><div>|-</div></td></tr>
<tr><td class='diff-marker'>−</td><td style="background: #ffa; color:black; font-size: smaller;"><div>| ChIPBase || total: <del class="diffchange diffchange-inline">4290 </del><br/> human: 2498 || total: <del class="diffchange diffchange-inline">Unknown </del><br/> human: Unknown || <i>H. sapiens, M. musculus, R. norvegicus, <br/> D. rerio, X. tropicalis, C. elegans, <br/> D. melanogaster, S. cerevisiae, A. thaliana, <br/> G. gallus</i> || >10 in total, but no uniform pipeline, <br/> each ChIP-seq is processed by different peak caller  || No</div></td><td class='diff-marker'>+</td><td style="background: #cfc; color:black; font-size: smaller;"><div>| ChIPBase || total: <ins class="diffchange diffchange-inline">4300 </ins><br/> human: 2498 || total: <ins class="diffchange diffchange-inline">870 </ins><br/> human: Unknown || <i>H. sapiens, M. musculus, R. norvegicus, <br/> D. rerio, X. tropicalis, C. elegans, <br/> D. melanogaster, S. cerevisiae, A. thaliana, <br/> G. gallus</i> || >10 in total, but no uniform pipeline, <br/> each ChIP-seq is processed by different peak caller  || No</div></td></tr>
<tr><td class='diff-marker'> </td><td style="background: #eee; color:black; font-size: smaller;"><div>|-</div></td><td class='diff-marker'> </td><td style="background: #eee; color:black; font-size: smaller;"><div>|-</div></td></tr>
<tr><td class='diff-marker'> </td><td style="background: #eee; color:black; font-size: smaller;"><div>| Factorbook || total: 1007 <br/> human: 837 || total: 167 <br/> human: 51 || <i>H. sapiens, M. musculus</i> || None || No</div></td><td class='diff-marker'> </td><td style="background: #eee; color:black; font-size: smaller;"><div>| Factorbook || total: 1007 <br/> human: 837 || total: 167 <br/> human: 51 || <i>H. sapiens, M. musculus</i> || None || No</div></td></tr>
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<tr><td class='diff-marker'> </td><td style="background: #eee; color:black; font-size: smaller;"><div>|}</div></td><td class='diff-marker'> </td><td style="background: #eee; color:black; font-size: smaller;"><div>|}</div></td></tr>
<tr><td class='diff-marker'> </td><td style="background: #eee; color:black; font-size: smaller;"></td><td class='diff-marker'> </td><td style="background: #eee; color:black; font-size: smaller;"></td></tr>
<tr><td class='diff-marker'>−</td><td style="background: #ffa; color:black; font-size: smaller;"><div><nowiki>*</nowiki>The number of ChIP-seq samples cannot be directly compared between databases as definition of sample may be distinct.</div></td><td class='diff-marker'>+</td><td style="background: #cfc; color:black; font-size: smaller;"><div><nowiki><ins class="diffchange diffchange-inline">*</ins>*</nowiki>The number of ChIP-seq samples cannot be directly compared between databases as definition of sample may be distinct.</div></td></tr>
</table>
Semyonk@dote.ru
https://wiki.biouml.org/index.php?title=GTRD_comparison&diff=8426&oldid=prev
Semyonk@dote.ru at 04:00, 8 November 2019
2019-11-08T04:00:51Z
<p></p>
<table class='diff diff-contentalign-left'>
<col class='diff-marker' />
<col class='diff-content' />
<col class='diff-marker' />
<col class='diff-content' />
<tr style='vertical-align: top;'>
<td colspan='2' style="background-color: white; color:black;">← Older revision</td>
<td colspan='2' style="background-color: white; color:black;">Revision as of 04:00, 8 November 2019</td>
</tr><tr><td colspan="2" class="diff-lineno">Line 2:</td>
<td colspan="2" class="diff-lineno">Line 2:</td></tr>
<tr><td class='diff-marker'> </td><td style="background: #eee; color:black; font-size: smaller;"><div>! Database !! Number of TF ChIP-seq samples !! Number of TF ( * - and others ) !! Species !! ChIP-seq peak callers !! Metacluster approach</div></td><td class='diff-marker'> </td><td style="background: #eee; color:black; font-size: smaller;"><div>! Database !! Number of TF ChIP-seq samples !! Number of TF ( * - and others ) !! Species !! ChIP-seq peak callers !! Metacluster approach</div></td></tr>
<tr><td class='diff-marker'> </td><td style="background: #eee; color:black; font-size: smaller;"><div>|-</div></td><td class='diff-marker'> </td><td style="background: #eee; color:black; font-size: smaller;"><div>|-</div></td></tr>
<tr><td class='diff-marker'>−</td><td style="background: #ffa; color:black; font-size: smaller;"><div>| GTRD v19.10 || total: 30670 <br/> human: 13515 || total: 3376 <br/> human: 1339 || H. sapiens, M. musculus, R. norvegicus, <br/> D. melanogaster, C. elegans, D. rerio, <br/> S. pombe, S. cerevisiae, A. thaliana || MACS2, SISSRs, GEM, PICS || Yes   </div></td><td class='diff-marker'>+</td><td style="background: #cfc; color:black; font-size: smaller;"><div>| GTRD v19.10 || total: 30670 <br/> human: 13515 || total: 3376 <br/> human: 1339 || <ins class="diffchange diffchange-inline"><i></ins>H. sapiens, M. musculus, R. norvegicus, <br/> D. melanogaster, C. elegans, D. rerio, <br/> S. pombe, S. cerevisiae, A. thaliana<ins class="diffchange diffchange-inline"></i> </ins>|| MACS2, SISSRs, GEM, PICS || Yes   </div></td></tr>
<tr><td class='diff-marker'> </td><td style="background: #eee; color:black; font-size: smaller;"><div>|-</div></td><td class='diff-marker'> </td><td style="background: #eee; color:black; font-size: smaller;"><div>|-</div></td></tr>
<tr><td class='diff-marker'>−</td><td style="background: #ffa; color:black; font-size: smaller;"><div>| ChIP-Atlas || total: 19414* <br/> human: 8368* || total: 1929 <br/> human: 820 || H. sapiens, M. musculus, R. norvegicus, <br/> D. melanogaster, C. elegans, S. cerevisiae || MACS2 || No</div></td><td class='diff-marker'>+</td><td style="background: #cfc; color:black; font-size: smaller;"><div>| ChIP-Atlas || total: 19414* <br/> human: 8368* || total: 1929 <br/> human: 820 || <ins class="diffchange diffchange-inline"><i></ins>H. sapiens, M. musculus, R. norvegicus, <br/> D. melanogaster, C. elegans, S. cerevisiae<ins class="diffchange diffchange-inline"></i> </ins>|| MACS2 || No</div></td></tr>
<tr><td class='diff-marker'> </td><td style="background: #eee; color:black; font-size: smaller;"><div>|-</div></td><td class='diff-marker'> </td><td style="background: #eee; color:black; font-size: smaller;"><div>|-</div></td></tr>
<tr><td class='diff-marker'>−</td><td style="background: #ffa; color:black; font-size: smaller;"><div>| Cistrome DB || total: 20408* <br/> human: 11348* || total: Unknown <br/>  human: Unknown || H. sapiens, M. musculus || MACS2 || No</div></td><td class='diff-marker'>+</td><td style="background: #cfc; color:black; font-size: smaller;"><div>| Cistrome DB || total: 20408* <br/> human: 11348* || total: Unknown <br/>  human: Unknown || <ins class="diffchange diffchange-inline"><i></ins>H. sapiens, M. musculus<ins class="diffchange diffchange-inline"></i> </ins>|| MACS2 || No</div></td></tr>
<tr><td class='diff-marker'> </td><td style="background: #eee; color:black; font-size: smaller;"><div>|-</div></td><td class='diff-marker'> </td><td style="background: #eee; color:black; font-size: smaller;"><div>|-</div></td></tr>
<tr><td class='diff-marker'>−</td><td style="background: #ffa; color:black; font-size: smaller;"><div>| ReMap 2018 || total: 2829* <br/> human: 2829* || total: 485 <br/> human: 485 || H. sapiens || MACS2 || Yes (CRMs)</div></td><td class='diff-marker'>+</td><td style="background: #cfc; color:black; font-size: smaller;"><div>| ReMap 2018 || total: 2829* <br/> human: 2829* || total: 485 <br/> human: 485 || <ins class="diffchange diffchange-inline"><i></ins>H. sapiens<ins class="diffchange diffchange-inline"></i> </ins>|| MACS2 || Yes (CRMs)</div></td></tr>
<tr><td class='diff-marker'> </td><td style="background: #eee; color:black; font-size: smaller;"><div>|-</div></td><td class='diff-marker'> </td><td style="background: #eee; color:black; font-size: smaller;"><div>|-</div></td></tr>
<tr><td class='diff-marker'>−</td><td style="background: #ffa; color:black; font-size: smaller;"><div>| ENCODE || total: 3684 <br/> human: 2489 || total: Unknown <br/> human: Unknown || H. sapiens, M. musculus, D. melanogaster, <br/> C. elegans || SPP || No</div></td><td class='diff-marker'>+</td><td style="background: #cfc; color:black; font-size: smaller;"><div>| ENCODE || total: 3684 <br/> human: 2489 || total: Unknown <br/> human: Unknown || <ins class="diffchange diffchange-inline"><i></ins>H. sapiens, M. musculus, D. melanogaster, <br/> C. elegans<ins class="diffchange diffchange-inline"></i> </ins>|| SPP || No</div></td></tr>
<tr><td class='diff-marker'> </td><td style="background: #eee; color:black; font-size: smaller;"><div>|-</div></td><td class='diff-marker'> </td><td style="background: #eee; color:black; font-size: smaller;"><div>|-</div></td></tr>
<tr><td class='diff-marker'>−</td><td style="background: #ffa; color:black; font-size: smaller;"><div>| ChIPBase || total: 4290 <br/> human: 2498 || total: Unknown <br/> human: Unknown || H. sapiens, M. musculus, R. norvegicus, <br/> D. rerio, X. tropicalis, C. elegans, <br/> D. melanogaster, S. cerevisiae, A. thaliana, <br/> G. gallus || >10 in total, but no uniform pipeline, <br/> each ChIP-seq is processed by different peak caller  || No</div></td><td class='diff-marker'>+</td><td style="background: #cfc; color:black; font-size: smaller;"><div>| ChIPBase || total: 4290 <br/> human: 2498 || total: Unknown <br/> human: Unknown || <ins class="diffchange diffchange-inline"><i></ins>H. sapiens, M. musculus, R. norvegicus, <br/> D. rerio, X. tropicalis, C. elegans, <br/> D. melanogaster, S. cerevisiae, A. thaliana, <br/> G. gallus<ins class="diffchange diffchange-inline"></i> </ins>|| >10 in total, but no uniform pipeline, <br/> each ChIP-seq is processed by different peak caller  || No</div></td></tr>
<tr><td class='diff-marker'> </td><td style="background: #eee; color:black; font-size: smaller;"><div>|-</div></td><td class='diff-marker'> </td><td style="background: #eee; color:black; font-size: smaller;"><div>|-</div></td></tr>
<tr><td class='diff-marker'>−</td><td style="background: #ffa; color:black; font-size: smaller;"><div>| Factorbook || total: 1007 <br/> human: 837 || total: 167 <br/> human: 51 || H. sapiens, M. musculus || None || No</div></td><td class='diff-marker'>+</td><td style="background: #cfc; color:black; font-size: smaller;"><div>| Factorbook || total: 1007 <br/> human: 837 || total: 167 <br/> human: 51 || <ins class="diffchange diffchange-inline"><i></ins>H. sapiens, M. musculus<ins class="diffchange diffchange-inline"></i> </ins>|| None || No</div></td></tr>
<tr><td class='diff-marker'> </td><td style="background: #eee; color:black; font-size: smaller;"><div>|-</div></td><td class='diff-marker'> </td><td style="background: #eee; color:black; font-size: smaller;"><div>|-</div></td></tr>
<tr><td class='diff-marker'>−</td><td style="background: #ffa; color:black; font-size: smaller;"><div>| NGS-QC || total: 22398 <br/> human: 11597 || total: Unkonwn <br/> human: Unknown || H. sapiens, M. musculus, R. norvegicus, <br/> D. rerio, C. elegans, D. melanogaster, <br/> S. cerevisiae, A. thaliana, G. gallus, <br/> P. troglodytes || None || No</div></td><td class='diff-marker'>+</td><td style="background: #cfc; color:black; font-size: smaller;"><div>| NGS-QC || total: 22398 <br/> human: 11597 || total: Unkonwn <br/> human: Unknown || <ins class="diffchange diffchange-inline"><i></ins>H. sapiens, M. musculus, R. norvegicus, <br/> D. rerio, C. elegans, D. melanogaster, <br/> S. cerevisiae, A. thaliana, G. gallus, <br/> P. troglodytes<ins class="diffchange diffchange-inline"></i> </ins>|| None || No</div></td></tr>
<tr><td class='diff-marker'> </td><td style="background: #eee; color:black; font-size: smaller;"><div>|}</div></td><td class='diff-marker'> </td><td style="background: #eee; color:black; font-size: smaller;"><div>|}</div></td></tr>
<tr><td class='diff-marker'> </td><td style="background: #eee; color:black; font-size: smaller;"></td><td class='diff-marker'> </td><td style="background: #eee; color:black; font-size: smaller;"></td></tr>
<tr><td class='diff-marker'> </td><td style="background: #eee; color:black; font-size: smaller;"><div><nowiki>*</nowiki>The number of ChIP-seq samples cannot be directly compared between databases as definition of sample may be distinct.</div></td><td class='diff-marker'> </td><td style="background: #eee; color:black; font-size: smaller;"><div><nowiki>*</nowiki>The number of ChIP-seq samples cannot be directly compared between databases as definition of sample may be distinct.</div></td></tr>
</table>
Semyonk@dote.ru
https://wiki.biouml.org/index.php?title=GTRD_comparison&diff=8425&oldid=prev
Semyonk@dote.ru at 03:58, 8 November 2019
2019-11-08T03:58:03Z
<p></p>
<table class='diff diff-contentalign-left'>
<col class='diff-marker' />
<col class='diff-content' />
<col class='diff-marker' />
<col class='diff-content' />
<tr style='vertical-align: top;'>
<td colspan='2' style="background-color: white; color:black;">← Older revision</td>
<td colspan='2' style="background-color: white; color:black;">Revision as of 03:58, 8 November 2019</td>
</tr><tr><td colspan="2" class="diff-lineno">Line 1:</td>
<td colspan="2" class="diff-lineno">Line 1:</td></tr>
<tr><td class='diff-marker'> </td><td style="background: #eee; color:black; font-size: smaller;"><div>{| class="wikitable"</div></td><td class='diff-marker'> </td><td style="background: #eee; color:black; font-size: smaller;"><div>{| class="wikitable"</div></td></tr>
<tr><td class='diff-marker'>−</td><td style="background: #ffa; color:black; font-size: smaller;"><div>! Database !! Number of TF ChIP-seq samples <del class="diffchange diffchange-inline">( * - and others ) </del>!! Number of TF ( * - and others ) !! Species !! ChIP-seq peak callers !! Metacluster approach</div></td><td class='diff-marker'>+</td><td style="background: #cfc; color:black; font-size: smaller;"><div>! Database !! Number of TF ChIP-seq samples !! Number of TF ( * - and others ) !! Species !! ChIP-seq peak callers !! Metacluster approach</div></td></tr>
<tr><td class='diff-marker'> </td><td style="background: #eee; color:black; font-size: smaller;"><div>|-</div></td><td class='diff-marker'> </td><td style="background: #eee; color:black; font-size: smaller;"><div>|-</div></td></tr>
<tr><td class='diff-marker'> </td><td style="background: #eee; color:black; font-size: smaller;"><div>| GTRD v19.10 || total: 30670 <br/> human: 13515 || total: 3376 <br/> human: 1339 || H. sapiens, M. musculus, R. norvegicus, <br/> D. melanogaster, C. elegans, D. rerio, <br/> S. pombe, S. cerevisiae, A. thaliana || MACS2, SISSRs, GEM, PICS || Yes   </div></td><td class='diff-marker'> </td><td style="background: #eee; color:black; font-size: smaller;"><div>| GTRD v19.10 || total: 30670 <br/> human: 13515 || total: 3376 <br/> human: 1339 || H. sapiens, M. musculus, R. norvegicus, <br/> D. melanogaster, C. elegans, D. rerio, <br/> S. pombe, S. cerevisiae, A. thaliana || MACS2, SISSRs, GEM, PICS || Yes   </div></td></tr>
</table>
Semyonk@dote.ru
https://wiki.biouml.org/index.php?title=GTRD_comparison&diff=8424&oldid=prev
Semyonk@dote.ru at 03:51, 8 November 2019
2019-11-08T03:51:48Z
<p></p>
<table class='diff diff-contentalign-left'>
<col class='diff-marker' />
<col class='diff-content' />
<col class='diff-marker' />
<col class='diff-content' />
<tr style='vertical-align: top;'>
<td colspan='2' style="background-color: white; color:black;">← Older revision</td>
<td colspan='2' style="background-color: white; color:black;">Revision as of 03:51, 8 November 2019</td>
</tr><tr><td colspan="2" class="diff-lineno">Line 2:</td>
<td colspan="2" class="diff-lineno">Line 2:</td></tr>
<tr><td class='diff-marker'> </td><td style="background: #eee; color:black; font-size: smaller;"><div>! Database !! Number of TF ChIP-seq samples ( * - and others ) !! Number of TF ( * - and others ) !! Species !! ChIP-seq peak callers !! Metacluster approach</div></td><td class='diff-marker'> </td><td style="background: #eee; color:black; font-size: smaller;"><div>! Database !! Number of TF ChIP-seq samples ( * - and others ) !! Number of TF ( * - and others ) !! Species !! ChIP-seq peak callers !! Metacluster approach</div></td></tr>
<tr><td class='diff-marker'> </td><td style="background: #eee; color:black; font-size: smaller;"><div>|-</div></td><td class='diff-marker'> </td><td style="background: #eee; color:black; font-size: smaller;"><div>|-</div></td></tr>
<tr><td class='diff-marker'>−</td><td style="background: #ffa; color:black; font-size: smaller;"><div>| GTRD <del class="diffchange diffchange-inline">v18</del>.<del class="diffchange diffchange-inline">06 </del>|| total: <del class="diffchange diffchange-inline">17485 </del><br/> human: <del class="diffchange diffchange-inline">7239 </del>|| total: <del class="diffchange diffchange-inline">2399 </del><br/> human: <del class="diffchange diffchange-inline">852 </del>|| H. sapiens, M. musculus, R. norvegicus, <br/> D. melanogaster, C. elegans, D. rerio, <br/> S. pombe, S. cerevisiae, A. thaliana || <del class="diffchange diffchange-inline">MACS</del>, SISSRs, GEM, PICS || Yes   </div></td><td class='diff-marker'>+</td><td style="background: #cfc; color:black; font-size: smaller;"><div>| GTRD <ins class="diffchange diffchange-inline">v19</ins>.<ins class="diffchange diffchange-inline">10 </ins>|| total: <ins class="diffchange diffchange-inline">30670 </ins><br/> human: <ins class="diffchange diffchange-inline">13515 </ins>|| total: <ins class="diffchange diffchange-inline">3376 </ins><br/> human: <ins class="diffchange diffchange-inline">1339 </ins>|| H. sapiens, M. musculus, R. norvegicus, <br/> D. melanogaster, C. elegans, D. rerio, <br/> S. pombe, S. cerevisiae, A. thaliana || <ins class="diffchange diffchange-inline">MACS2</ins>, SISSRs, GEM, PICS || Yes   </div></td></tr>
<tr><td class='diff-marker'> </td><td style="background: #eee; color:black; font-size: smaller;"><div>|-</div></td><td class='diff-marker'> </td><td style="background: #eee; color:black; font-size: smaller;"><div>|-</div></td></tr>
<tr><td class='diff-marker'> </td><td style="background: #eee; color:black; font-size: smaller;"><div>| ChIP-Atlas || total: 19414* <br/> human: 8368* || total: 1929 <br/> human: 820 || H. sapiens, M. musculus, R. norvegicus, <br/> D. melanogaster, C. elegans, S. cerevisiae || MACS2 || No</div></td><td class='diff-marker'> </td><td style="background: #eee; color:black; font-size: smaller;"><div>| ChIP-Atlas || total: 19414* <br/> human: 8368* || total: 1929 <br/> human: 820 || H. sapiens, M. musculus, R. norvegicus, <br/> D. melanogaster, C. elegans, S. cerevisiae || MACS2 || No</div></td></tr>
<tr><td colspan="2" class="diff-lineno">Line 10:</td>
<td colspan="2" class="diff-lineno">Line 10:</td></tr>
<tr><td class='diff-marker'> </td><td style="background: #eee; color:black; font-size: smaller;"><div>| ReMap 2018 || total: 2829* <br/> human: 2829* || total: 485 <br/> human: 485 || H. sapiens || MACS2 || Yes (CRMs)</div></td><td class='diff-marker'> </td><td style="background: #eee; color:black; font-size: smaller;"><div>| ReMap 2018 || total: 2829* <br/> human: 2829* || total: 485 <br/> human: 485 || H. sapiens || MACS2 || Yes (CRMs)</div></td></tr>
<tr><td class='diff-marker'> </td><td style="background: #eee; color:black; font-size: smaller;"><div>|-</div></td><td class='diff-marker'> </td><td style="background: #eee; color:black; font-size: smaller;"><div>|-</div></td></tr>
<tr><td class='diff-marker'>−</td><td style="background: #ffa; color:black; font-size: smaller;"><div>| ENCODE || total: 3684 <br/> human: 2489 || total: Unknown <br/> human: Unknown || H. sapiens, M. musculus, D. melanogaster, <br/> C. elegans || SPP<del class="diffchange diffchange-inline">, GEM, PeakSeq, MACS </del>|| No</div></td><td class='diff-marker'>+</td><td style="background: #cfc; color:black; font-size: smaller;"><div>| ENCODE || total: 3684 <br/> human: 2489 || total: Unknown <br/> human: Unknown || H. sapiens, M. musculus, D. melanogaster, <br/> C. elegans || SPP || No</div></td></tr>
<tr><td class='diff-marker'> </td><td style="background: #eee; color:black; font-size: smaller;"><div>|-</div></td><td class='diff-marker'> </td><td style="background: #eee; color:black; font-size: smaller;"><div>|-</div></td></tr>
<tr><td class='diff-marker'> </td><td style="background: #eee; color:black; font-size: smaller;"><div>| ChIPBase || total: 4290 <br/> human: 2498 || total: Unknown <br/> human: Unknown || H. sapiens, M. musculus, R. norvegicus, <br/> D. rerio, X. tropicalis, C. elegans, <br/> D. melanogaster, S. cerevisiae, A. thaliana, <br/> G. gallus || >10 in total, but no uniform pipeline, <br/> each ChIP-seq is processed by different peak caller  || No</div></td><td class='diff-marker'> </td><td style="background: #eee; color:black; font-size: smaller;"><div>| ChIPBase || total: 4290 <br/> human: 2498 || total: Unknown <br/> human: Unknown || H. sapiens, M. musculus, R. norvegicus, <br/> D. rerio, X. tropicalis, C. elegans, <br/> D. melanogaster, S. cerevisiae, A. thaliana, <br/> G. gallus || >10 in total, but no uniform pipeline, <br/> each ChIP-seq is processed by different peak caller  || No</div></td></tr>
</table>
Semyonk@dote.ru
https://wiki.biouml.org/index.php?title=GTRD_comparison&diff=7601&oldid=prev
Semyonk@dote.ru at 04:20, 13 November 2018
2018-11-13T04:20:20Z
<p></p>
<table class='diff diff-contentalign-left'>
<col class='diff-marker' />
<col class='diff-content' />
<col class='diff-marker' />
<col class='diff-content' />
<tr style='vertical-align: top;'>
<td colspan='2' style="background-color: white; color:black;">← Older revision</td>
<td colspan='2' style="background-color: white; color:black;">Revision as of 04:20, 13 November 2018</td>
</tr><tr><td colspan="2" class="diff-lineno">Line 2:</td>
<td colspan="2" class="diff-lineno">Line 2:</td></tr>
<tr><td class='diff-marker'> </td><td style="background: #eee; color:black; font-size: smaller;"><div>! Database !! Number of TF ChIP-seq samples ( * - and others ) !! Number of TF ( * - and others ) !! Species !! ChIP-seq peak callers !! Metacluster approach</div></td><td class='diff-marker'> </td><td style="background: #eee; color:black; font-size: smaller;"><div>! Database !! Number of TF ChIP-seq samples ( * - and others ) !! Number of TF ( * - and others ) !! Species !! ChIP-seq peak callers !! Metacluster approach</div></td></tr>
<tr><td class='diff-marker'> </td><td style="background: #eee; color:black; font-size: smaller;"><div>|-</div></td><td class='diff-marker'> </td><td style="background: #eee; color:black; font-size: smaller;"><div>|-</div></td></tr>
<tr><td class='diff-marker'>−</td><td style="background: #ffa; color:black; font-size: smaller;"><div>| GTRD v18.06 || total: 17485 <br/> human: 7239 || total: 2399 <br/> human: 852 || H. sapiens, M. musculus, R. norvegicus, D. melanogaster, C. elegans, D. rerio, S. pombe, S. cerevisiae, A. thaliana || MACS, SISSRs, GEM, PICS || Yes   </div></td><td class='diff-marker'>+</td><td style="background: #cfc; color:black; font-size: smaller;"><div>| GTRD v18.06 || total: 17485 <br/> human: 7239 || total: 2399 <br/> human: 852 || H. sapiens, M. musculus, R. norvegicus, <ins class="diffchange diffchange-inline"><br/> </ins>D. melanogaster, C. elegans, D. rerio, <ins class="diffchange diffchange-inline"><br/> </ins>S. pombe, S. cerevisiae, A. thaliana || MACS, SISSRs, GEM, PICS || Yes   </div></td></tr>
<tr><td class='diff-marker'> </td><td style="background: #eee; color:black; font-size: smaller;"><div>|-</div></td><td class='diff-marker'> </td><td style="background: #eee; color:black; font-size: smaller;"><div>|-</div></td></tr>
<tr><td class='diff-marker'>−</td><td style="background: #ffa; color:black; font-size: smaller;"><div>| ChIP-Atlas || total: 19414* <br/> human: 8368* || total: 1929 <br/> human: 820 || H. sapiens, M. musculus, R. norvegicus, D. melanogaster, C. elegans, S. cerevisiae || MACS2 || No</div></td><td class='diff-marker'>+</td><td style="background: #cfc; color:black; font-size: smaller;"><div>| ChIP-Atlas || total: 19414* <br/> human: 8368* || total: 1929 <br/> human: 820 || H. sapiens, M. musculus, R. norvegicus, <ins class="diffchange diffchange-inline"><br/> </ins>D. melanogaster, C. elegans, S. cerevisiae || MACS2 || No</div></td></tr>
<tr><td class='diff-marker'> </td><td style="background: #eee; color:black; font-size: smaller;"><div>|-</div></td><td class='diff-marker'> </td><td style="background: #eee; color:black; font-size: smaller;"><div>|-</div></td></tr>
<tr><td class='diff-marker'> </td><td style="background: #eee; color:black; font-size: smaller;"><div>| Cistrome DB || total: 20408* <br/> human: 11348* || total: Unknown <br/>  human: Unknown || H. sapiens, M. musculus || MACS2 || No</div></td><td class='diff-marker'> </td><td style="background: #eee; color:black; font-size: smaller;"><div>| Cistrome DB || total: 20408* <br/> human: 11348* || total: Unknown <br/>  human: Unknown || H. sapiens, M. musculus || MACS2 || No</div></td></tr>
<tr><td colspan="2" class="diff-lineno">Line 10:</td>
<td colspan="2" class="diff-lineno">Line 10:</td></tr>
<tr><td class='diff-marker'> </td><td style="background: #eee; color:black; font-size: smaller;"><div>| ReMap 2018 || total: 2829* <br/> human: 2829* || total: 485 <br/> human: 485 || H. sapiens || MACS2 || Yes (CRMs)</div></td><td class='diff-marker'> </td><td style="background: #eee; color:black; font-size: smaller;"><div>| ReMap 2018 || total: 2829* <br/> human: 2829* || total: 485 <br/> human: 485 || H. sapiens || MACS2 || Yes (CRMs)</div></td></tr>
<tr><td class='diff-marker'> </td><td style="background: #eee; color:black; font-size: smaller;"><div>|-</div></td><td class='diff-marker'> </td><td style="background: #eee; color:black; font-size: smaller;"><div>|-</div></td></tr>
<tr><td class='diff-marker'>−</td><td style="background: #ffa; color:black; font-size: smaller;"><div>| ENCODE || total: 3684 <br/> human: 2489 || total: Unknown <br/> human: Unknown || H. sapiens, M. musculus, D. melanogaster, C. elegans || SPP, GEM, PeakSeq, MACS || No</div></td><td class='diff-marker'>+</td><td style="background: #cfc; color:black; font-size: smaller;"><div>| ENCODE || total: 3684 <br/> human: 2489 || total: Unknown <br/> human: Unknown || H. sapiens, M. musculus, D. melanogaster, <ins class="diffchange diffchange-inline"><br/> </ins>C. elegans || SPP, GEM, PeakSeq, MACS || No</div></td></tr>
<tr><td class='diff-marker'> </td><td style="background: #eee; color:black; font-size: smaller;"><div>|-</div></td><td class='diff-marker'> </td><td style="background: #eee; color:black; font-size: smaller;"><div>|-</div></td></tr>
<tr><td class='diff-marker'>−</td><td style="background: #ffa; color:black; font-size: smaller;"><div>| ChIPBase || total: 4290 <br/> human: 2498 || total: Unknown <br/> human: Unknown || H. sapiens, M. musculus, R. norvegicus, D. rerio, X. tropicalis, C. elegans, D. melanogaster, S. cerevisiae, A. thaliana, G. gallus || >10 in total, but no uniform pipeline, each ChIP-seq is processed by different peak caller  || No</div></td><td class='diff-marker'>+</td><td style="background: #cfc; color:black; font-size: smaller;"><div>| ChIPBase || total: 4290 <br/> human: 2498 || total: Unknown <br/> human: Unknown || H. sapiens, M. musculus, R. norvegicus, <ins class="diffchange diffchange-inline"><br/> </ins>D. rerio, X. tropicalis, C. elegans, <ins class="diffchange diffchange-inline"><br/> </ins>D. melanogaster, S. cerevisiae, A. thaliana, <ins class="diffchange diffchange-inline"><br/> </ins>G. gallus || >10 in total, but no uniform pipeline, <ins class="diffchange diffchange-inline"><br/> </ins>each ChIP-seq is processed by different peak caller  || No</div></td></tr>
<tr><td class='diff-marker'> </td><td style="background: #eee; color:black; font-size: smaller;"><div>|-</div></td><td class='diff-marker'> </td><td style="background: #eee; color:black; font-size: smaller;"><div>|-</div></td></tr>
<tr><td class='diff-marker'> </td><td style="background: #eee; color:black; font-size: smaller;"><div>| Factorbook || total: 1007 <br/> human: 837 || total: 167 <br/> human: 51 || H. sapiens, M. musculus || None || No</div></td><td class='diff-marker'> </td><td style="background: #eee; color:black; font-size: smaller;"><div>| Factorbook || total: 1007 <br/> human: 837 || total: 167 <br/> human: 51 || H. sapiens, M. musculus || None || No</div></td></tr>
<tr><td class='diff-marker'> </td><td style="background: #eee; color:black; font-size: smaller;"><div>|-</div></td><td class='diff-marker'> </td><td style="background: #eee; color:black; font-size: smaller;"><div>|-</div></td></tr>
<tr><td class='diff-marker'>−</td><td style="background: #ffa; color:black; font-size: smaller;"><div>| NGS-QC || total: 22398 <br/> human: 11597 || total: Unkonwn <br/> human: Unknown || H. sapiens, M. musculus, R. norvegicus, D. rerio, C. elegans, D. melanogaster, S. cerevisiae, A. thaliana, G. gallus, P. troglodytes || None || No</div></td><td class='diff-marker'>+</td><td style="background: #cfc; color:black; font-size: smaller;"><div>| NGS-QC || total: 22398 <br/> human: 11597 || total: Unkonwn <br/> human: Unknown || H. sapiens, M. musculus, R. norvegicus, <ins class="diffchange diffchange-inline"><br/> </ins>D. rerio, C. elegans, D. melanogaster, <ins class="diffchange diffchange-inline"><br/> </ins>S. cerevisiae, A. thaliana, G. gallus, <ins class="diffchange diffchange-inline"><br/> </ins>P. troglodytes || None || No</div></td></tr>
<tr><td class='diff-marker'> </td><td style="background: #eee; color:black; font-size: smaller;"><div>|}</div></td><td class='diff-marker'> </td><td style="background: #eee; color:black; font-size: smaller;"><div>|}</div></td></tr>
<tr><td class='diff-marker'> </td><td style="background: #eee; color:black; font-size: smaller;"></td><td class='diff-marker'> </td><td style="background: #eee; color:black; font-size: smaller;"></td></tr>
<tr><td class='diff-marker'> </td><td style="background: #eee; color:black; font-size: smaller;"><div><nowiki>*</nowiki>The number of ChIP-seq samples cannot be directly compared between databases as definition of sample may be distinct.</div></td><td class='diff-marker'> </td><td style="background: #eee; color:black; font-size: smaller;"><div><nowiki>*</nowiki>The number of ChIP-seq samples cannot be directly compared between databases as definition of sample may be distinct.</div></td></tr>
</table>
Semyonk@dote.ru