MCL coexpression mm9:1421: Difference between revisions
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{{MCL_coexpression_mm9 | 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modification;0.0278390932588522;19651!GO:0006325;establishment and/or maintenance of chromatin architecture;0.0278390932588522;19651!GO:0006323;DNA packaging;0.0278390932588522;19651!GO:0051276;chromosome organization and biogenesis;0.0278390932588522;19651!GO:0030426;growth cone;0.0278390932588522;338355!GO:0030427;site of polarized growth;0.0278390932588522;338355!GO:0006355;regulation of transcription, DNA-dependent;0.0278390932588522;319535,19651!GO:0006351;transcription, DNA-dependent;0.0278390932588522;319535,19651!GO:0032774;RNA biosynthetic process;0.0278390932588522;319535,19651!GO:0003677;DNA binding;0.0278390932588522;319535,19651!GO:0045449;regulation of transcription;0.0278390932588522;319535,19651!GO:0019219;regulation of nucleobase, nucleoside, nucleotide and nucleic acid metabolic process;0.0278390932588522;319535,19651!GO:0006350;transcription;0.0278390932588522;319535,19651!GO:0010468;regulation of gene expression;0.0278390932588522;319535,19651!GO:0005884;actin 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| ||
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| |||
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}} | |||
Latest revision as of 16:54, 17 September 2013
Phase1 CAGE Peaks
| Short description | |
|---|---|
| Mm9::chr19:61216675..61216726,- | p1@ENSMUST00000122927 p1@ENSMUST00000127117 p1@ENSMUST00000143264 p1@uc008icf.2 p1@uc008icg.2 p1@uc008ici.1 |
| Mm9::chr4:62021470..62021545,- | p1@Fkbp15 |
| Mm9::chr4:73897832..73897894,+ | p1@Kdm4c |
| Mm9::chr5:110295720..110295766,+ | p@chr5:110295720..110295766 + |
| Mm9::chr8:93593951..93594022,+ | p1@Rbl2 |
| Mm9::chrX:20639107..20639188,- | p1@Zfp182 |
Enriched pathways on this co-expression cluster<b>Summary:</b><br>Canonical pathway gene sets were compiled from Reactome, Wikipathways and KEGG. For the major signaling pathways, the transcriptionally-regulated genes (downstream targets) were obtained from Netpath. Combined, the canonical pathways and downstream targets totaled 489 human gene sets. The corresponding M. musculus gene sets were inferred by homology using the HomoloGene database. Enrichment for each of the canonical 489 pathways and gene sets included in the co-expression cluster was assessed by the hypergeometric probability. The resulting P values were also then adjusted by the Benjamini-Hochberg method for multiple comparisons.<br><b>Analyst: </b>Emmanuel Dimont<br><br>link to source dataset<br>data
| GO ID | GO name | FDR corrected p-value |
|---|---|---|
| GO:0016568 | chromatin modification | 0.0278390932588522 |
| GO:0006325 | establishment and/or maintenance of chromatin architecture | 0.0278390932588522 |
| GO:0006323 | DNA packaging | 0.0278390932588522 |
| GO:0051276 | chromosome organization and biogenesis | 0.0278390932588522 |
| GO:0030426 | growth cone | 0.0278390932588522 |
| GO:0030427 | site of polarized growth | 0.0278390932588522 |
| GO:0006355 | regulation of transcription, DNA-dependent | 0.0278390932588522 |
| GO:0006351 | transcription, DNA-dependent | 0.0278390932588522 |
| GO:0032774 | RNA biosynthetic process | 0.0278390932588522 |
| GO:0003677 | DNA binding | 0.0278390932588522 |
| GO:0045449 | regulation of transcription | 0.0278390932588522 |
| GO:0019219 | regulation of nucleobase, nucleoside, nucleotide and nucleic acid metabolic process | 0.0278390932588522 |
| GO:0006350 | transcription | 0.0278390932588522 |
| GO:0010468 | regulation of gene expression | 0.0278390932588522 |
| GO:0005884 | actin filament | 0.0278390932588522 |
| GO:0031323 | regulation of cellular metabolic process | 0.0281658112945624 |
| GO:0019222 | regulation of metabolic process | 0.0284271100944954 |
| GO:0006259 | DNA metabolic process | 0.0284271100944954 |
| GO:0016070 | RNA metabolic process | 0.0284271100944954 |
| GO:0043170 | macromolecule metabolic process | 0.0300812145158244 |
| GO:0010467 | gene expression | 0.0400737164773372 |
| GO:0003676 | nucleic acid binding | 0.0400737164773372 |
| GO:0044238 | primary metabolic process | 0.0400737164773372 |
| GO:0051213 | dioxygenase activity | 0.0400737164773372 |
| GO:0016702 | oxidoreductase activity, acting on single donors with incorporation of molecular oxygen, incorporation of two atoms of oxygen | 0.0400737164773372 |
| GO:0044237 | cellular metabolic process | 0.0400737164773372 |
| GO:0016701 | oxidoreductase activity, acting on single donors with incorporation of molecular oxygen | 0.0400737164773372 |
| GO:0030424 | axon | 0.0400737164773372 |
| GO:0006139 | nucleobase, nucleoside, nucleotide and nucleic acid metabolic process | 0.0415391950259398 |
| GO:0050794 | regulation of cellular process | 0.0490363897477721 |
Relative expression of the co-expression cluster over median <br>Analyst:
Enriched sample ontology terms on this co-expression cluster<b>Summary:</b>To summarize promoter activities (expression profile of a TSS region) across ~1000 samples, we performed enrichment analysis based on FANTOM5 Sample Ontology (FF ontology). The question here is “in which type of samples the promoter is more active”. To answer this question, we compared expressions (TPMs) in the samples associated with a sample ontology term and the rest of the samples by using the Mann-Whitney rank sum test. To summarize ontologies enriched in this co-expression cluster, we ran the same analysis on an averaged expression profile of all promoters that make up. <b>Analyst:</b> Hideya Kawaji <br><br>links to source dataset<br><br><br>uberon_data<br><br>
| Ontology term | p-value | n |
|---|---|---|
| adult organism | 4.73e-09 | 51 |
TFBS overrepresentation<b>Summary:</b>The values shown are the p-values for overrepresentation of the motif in this coexpression cluster. So a small p-value means a strong overrepresentation. <b>Analyst:</b> Michiel de Hoon <br><br>link to source data <br> Novel motifs <br>data <br><br> Jaspar motifs <br>data
Novel motifs
JASPAR motifs
| Motifs | -log10(p-value) |
|---|---|
| MA0003.1 | 0.276983 |
| MA0004.1 | 1.3269 |
| MA0006.1 | 0.945134 |
| MA0007.1 | 0.52077 |
| MA0009.1 | 0.987341 |
| MA0014.1 | 0.0315641 |
| MA0017.1 | 0.387481 |
| MA0019.1 | 0.800946 |
| MA0024.1 | 0.942716 |
| MA0025.1 | 1.22395 |
| MA0027.1 | 2.64231 |
| MA0028.1 | 0.969171 |
| MA0029.1 | 0.920529 |
| MA0030.1 | 0.927235 |
| MA0031.1 | 0.890871 |
| MA0038.1 | 1.64201 |
| MA0040.1 | 1.00009 |
| MA0041.1 | 1.15799 |
| MA0042.1 | 0.443591 |
| MA0043.1 | 1.08567 |
| MA0046.1 | 1.02391 |
| MA0048.1 | 0.486223 |
| MA0050.1 | 0.57678 |
| MA0051.1 | 0.695779 |
| MA0052.1 | 1.00829 |
| MA0055.1 | 0.212634 |
| MA0056.1 | 0 |
| MA0057.1 | 0.149949 |
| MA0058.1 | 1.94869 |
| MA0059.1 | 0.449345 |
| MA0060.1 | 2.1282 |
| MA0061.1 | 0.307097 |
| MA0063.1 | 0 |
| MA0066.1 | 0.675169 |
| MA0067.1 | 1.33603 |
| MA0068.1 | 0.153907 |
| MA0069.1 | 1.00864 |
| MA0070.1 | 0.998765 |
| MA0071.1 | 0.575909 |
| MA0072.1 | 0.990133 |
| MA0073.1 | 0.00140584 |
| MA0074.1 | 0.638014 |
| MA0076.1 | 0.407465 |
| MA0077.1 | 0.968053 |
| MA0078.1 | 0.729877 |
| MA0081.1 | 0.473489 |
| MA0083.1 | 1.08487 |
| MA0084.1 | 1.66561 |
| MA0087.1 | 1.04109 |
| MA0088.1 | 0.358337 |
| MA0089.1 | 0 |
| MA0090.1 | 0.500693 |
| MA0091.1 | 0.55008 |
| MA0092.1 | 0.501022 |
| MA0093.1 | 1.75322 |
| MA0095.1 | 0 |
| MA0098.1 | 0 |
| MA0100.1 | 0.626021 |
| MA0101.1 | 1.16089 |
| MA0103.1 | 0.398766 |
| MA0105.1 | 0.57901 |
| MA0106.1 | 0.737893 |
| MA0107.1 | 1.0169 |
| MA0108.2 | 0.824407 |
| MA0109.1 | 0 |
| MA0111.1 | 1.2824 |
| MA0113.1 | 0.708789 |
| MA0114.1 | 0.304661 |
| MA0115.1 | 1.08851 |
| MA0116.1 | 0.359483 |
| MA0117.1 | 1.05576 |
| MA0119.1 | 0.459301 |
| MA0122.1 | 1.07591 |
| MA0124.1 | 1.28237 |
| MA0125.1 | 1.20757 |
| MA0130.1 | 0 |
| MA0131.1 | 0.796279 |
| MA0132.1 | 0 |
| MA0133.1 | 0 |
| MA0135.1 | 1.1226 |
| MA0136.1 | 0.658622 |
| MA0139.1 | 0.243463 |
| MA0140.1 | 0.625902 |
| MA0141.1 | 0.419361 |
| MA0142.1 | 0.876028 |
| MA0143.1 | 0.725672 |
| MA0144.1 | 0.307873 |
| MA0145.1 | 0.119202 |
| MA0146.1 | 0.990842 |
| MA0147.1 | 0.320675 |
| MA0148.1 | 0.553294 |
| MA0149.1 | 0.464445 |
| MA0062.2 | 0.591842 |
| MA0035.2 | 0.630778 |
| MA0039.2 | 0.00481054 |
| MA0138.2 | 0.788113 |
| MA0002.2 | 0.246463 |
| MA0137.2 | 0.416331 |
| MA0104.2 | 2.05302 |
| MA0047.2 | 0.685741 |
| MA0112.2 | 0.119197 |
| MA0065.2 | 0.763394 |
| MA0150.1 | 0.520653 |
| MA0151.1 | 0 |
| MA0152.1 | 0.685852 |
| MA0153.1 | 1.13945 |
| MA0154.1 | 2.13869 |
| MA0155.1 | 0.132921 |
| MA0156.1 | 0.406559 |
| MA0157.1 | 0.843181 |
| MA0158.1 | 0 |
| MA0159.1 | 0.331229 |
| MA0160.1 | 0.556423 |
| MA0161.1 | 0 |
| MA0162.1 | 0.0465447 |
| MA0163.1 | 0.0423021 |
| MA0164.1 | 1.58466 |
| MA0080.2 | 1.01893 |
| MA0018.2 | 0.669032 |
| MA0099.2 | 0.781628 |
| MA0079.2 | 0.00464563 |
| MA0102.2 | 1.7182 |
| MA0258.1 | 0.790457 |
| MA0259.1 | 0.833237 |
| MA0442.1 | 0 |
