MCL coexpression mm9:1553: Difference between revisions
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|ontology_enrichment_disease= | |ontology_enrichment_disease= | ||
|ontology_enrichment_uberon=UBERON:0004177!1.04e-09!29;UBERON:0005057!1.04e-09!29;UBERON:0006562!7.28e-09!24;UBERON:0001557!7.28e-09!24;UBERON:0001042!7.28e-09!24;UBERON:0008814!7.28e-09!24;UBERON:0009145!7.28e-09!24;UBERON:0002370!1.23e-08!23;UBERON:0000974!1.23e-08!23;UBERON:0004807!1.23e-08!23;UBERON:0005058!1.23e-08!23;UBERON:0003351!1.23e-08!23;UBERON:0009113!1.23e-08!23;UBERON:0003295!1.23e-08!23;UBERON:0009722!1.23e-08!23;UBERON:0005562!1.23e-08!23;UBERON:0007690!1.23e-08!23;UBERON:0000153!1.70e-08!43;UBERON:0003408!3.12e-08!24;UBERON:0002020!1.46e-07!34;UBERON:0000064!1.59e-07!99;UBERON:0000077!1.67e-07!35;UBERON:0000072!5.20e-07!27;UBERON:0007811!6.96e-07!36 | |ontology_enrichment_uberon=UBERON:0004177!1.04e-09!29;UBERON:0005057!1.04e-09!29;UBERON:0006562!7.28e-09!24;UBERON:0001557!7.28e-09!24;UBERON:0001042!7.28e-09!24;UBERON:0008814!7.28e-09!24;UBERON:0009145!7.28e-09!24;UBERON:0002370!1.23e-08!23;UBERON:0000974!1.23e-08!23;UBERON:0004807!1.23e-08!23;UBERON:0005058!1.23e-08!23;UBERON:0003351!1.23e-08!23;UBERON:0009113!1.23e-08!23;UBERON:0003295!1.23e-08!23;UBERON:0009722!1.23e-08!23;UBERON:0005562!1.23e-08!23;UBERON:0007690!1.23e-08!23;UBERON:0000153!1.70e-08!43;UBERON:0003408!3.12e-08!24;UBERON:0002020!1.46e-07!34;UBERON:0000064!1.59e-07!99;UBERON:0000077!1.67e-07!35;UBERON:0000072!5.20e-07!27;UBERON:0007811!6.96e-07!36 | ||
|tfbs_overrepresentation_for_novel_motifs=0.557864,0.293744,0.529553,0.603273,0.406364,0.618805,0.715644,0.300268,0.836099,0.746305,0.668936,0.702872,1.47559,0.728641,0.424775,0,0.930881,0.397593,0.775038,0.185796,0.489529,0.145201,0.727684,0.404661,0.537749,1.78963,0.274609,0.641282,0.456327,0.227599,1.51608,1.03545,1.02297,0.253145,1.08876,0.454919,0.384813,0.699032,0.360612,0.876199,0.401916,0.631725,0.419293,0.426986,0.84962,0.591277,0.847828,0.658142,0.370501,1.16276,0.912738,3.0797,0.220111,1.18062,1.19842,0.73621,0.469329,0.689304,0.26467,1.74061,1.01481,0.796017,0.323911,0.901018,0.747985,0.943088,1.33705,1.68977,1.00999,1.54147,0.509047,0.30684,0.152094,1.23259,2.03319,0.245132,0.253065,0.835925,0.997094,0.494135,0.308173,0.948899,0.794502,0.293164,1.1148,0.0793594,1.53502,0.227755,3.28882,1.85284,1.40768,1.11989,1.04863,0.412897,0.356133,0.3366,0.297538,1.05152,1.97563,0.590368,0.384901,1.03517,1.16282,0.913356,0.91226,2.58845,3.66482,0.653843,0.499439,0.491483,1.35621,1.16464,0.495367,0.674448,1.41481,0.399936,0.328405,0.607321,0.932233,0.991416,1.23809,0.879184,0.759676,0.834976,1.46955,1.00091,0.724289,2.37077,1.33551,0.416189,1.14546,0.595426,1.3055,0.750642,1.43666,0.143464,1.39156,0.633235,1.3869,2.2222,1.82084,1.34183,0.772375,1.04623,0.905521,0.632211,0.851091,2.18247,0.569503,0.408309,0.651755,1.93643,1.18223,0.343194,0.749664,1.26545,0.787153,0.438007,0.555203,0.566652,1.39653,1.11392,1.00137,0.547782,0.90208,0.741834,0.383572,0.701187,1.60845 | |||
}} | }} | ||
Revision as of 20:05, 26 November 2012
Phase1 CAGE Peaks
| Short description | |
|---|---|
| Mm9::chr11:116704833..116704883,+ | p1@1110005A03Rik |
| Mm9::chr14:21208135..21208149,- | p2@Dnajc9 |
| Mm9::chr9:79641328..79641348,- | p2@Tmem30a |
| Mm9::chr9:79641352..79641378,- | p4@Tmem30a |
| Mm9::chrX:45866695..45866742,- | p2@Aifm1 |
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:0004174 | electron-transferring-flavoprotein dehydrogenase activity | 0.0203785365697633 |
| GO:0016649 | oxidoreductase activity, acting on the CH-NH group of donors, quinone or similar compound as acceptor | 0.0203785365697633 |
| GO:0006309 | DNA fragmentation during apoptosis | 0.0344301086670188 |
| GO:0006921 | cell structure disassembly during apoptosis | 0.0344301086670188 |
| GO:0030262 | apoptotic nuclear changes | 0.0344301086670188 |
| GO:0005758 | mitochondrial intermembrane space | 0.0344301086670188 |
| GO:0006308 | DNA catabolic process | 0.0344301086670188 |
| GO:0005741 | mitochondrial outer membrane | 0.0344301086670188 |
| GO:0008637 | apoptotic mitochondrial changes | 0.0344301086670188 |
| GO:0016645 | oxidoreductase activity, acting on the CH-NH group of donors | 0.0344301086670188 |
| GO:0031970 | organelle envelope lumen | 0.0344301086670188 |
| GO:0031968 | organelle outer membrane | 0.0344301086670188 |
| GO:0022411 | cellular component disassembly | 0.0344301086670188 |
| GO:0006997 | nuclear organization and biogenesis | 0.037771268991134 |
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 |
|---|---|---|
| hemopoietic organ | 1.04e-09 | 29 |
| immune organ | 1.04e-09 | 29 |
| pharynx | 7.28e-09 | 24 |
| upper respiratory tract | 7.28e-09 | 24 |
| chordate pharynx | 7.28e-09 | 24 |
| pharyngeal arch system | 7.28e-09 | 24 |
| pharyngeal region of foregut | 7.28e-09 | 24 |
| thymus | 1.23e-08 | 23 |
| neck | 1.23e-08 | 23 |
| respiratory system epithelium | 1.23e-08 | 23 |
| hemolymphoid system gland | 1.23e-08 | 23 |
| pharyngeal epithelium | 1.23e-08 | 23 |
| thymic region | 1.23e-08 | 23 |
| pharyngeal gland | 1.23e-08 | 23 |
| entire pharyngeal arch endoderm | 1.23e-08 | 23 |
| thymus primordium | 1.23e-08 | 23 |
| early pharyngeal endoderm | 1.23e-08 | 23 |
| anterior region of body | 1.70e-08 | 43 |
| gland of gut | 3.12e-08 | 24 |
| gray matter | 1.46e-07 | 34 |
| organ part | 1.59e-07 | 99 |
| mixed endoderm/mesoderm-derived structure | 1.67e-07 | 35 |
| segment of respiratory tract | 5.20e-07 | 27 |
| craniocervical region | 6.96e-07 | 36 |
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) |
|---|---|
|
{{{tfbs_overrepresentation_jaspar}}} |
