Coexpression cluster:C29: Difference between revisions
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|tf_chipseq_enrich=STAT3#6774;86:1.45445979060332:0.000306297982836585:0.00315914033472942!ZNF274#10782;4:9.14306208261192:0.00103201747672837:0.00729988982404569 | |tf_chipseq_enrich=STAT3#6774;86:1.45445979060332:0.000306297982836585:0.00315914033472942!ZNF274#10782;4:9.14306208261192:0.00103201747672837:0.00729988982404569 | ||
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| ||
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}} | }} | ||
Revision as of 13:08, 26 November 2012
Full id: C29_mature_adipose_Adipocyte_breast_Lymphatic_vein_heart
Phase1 CAGE Peaks
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
| p.value | FDR | nGenes | nPathway | Name |
|---|---|---|---|---|
| 4.36700326500841e-06 | 0.000552862613350065 | 5 | 50 | Glycerolipid metabolism (KEGG):00561 |
| 4.96861367546277e-05 | 0.00314513245656793 | 5 | 82 | Glycerophospholipid metabolism (KEGG):00564 |
| 2.00124595961183e-09 | 6.33394346217144e-07 | 8 | 71 | PPAR signaling pathway (KEGG):03320 |
| 2.15204315836991e-05 | 0.00194606188464022 | 5 | 69 | Adipocytokine signaling pathway (KEGG):04920 |
| 7.28800291137178e-05 | 0.00419391440263485 | 4 | 46 | Fat digestion and absorption (KEGG):04975 |
| 2.069401844406e-08 | 4.36643789169666e-06 | 9 | 135 | Adipogenesis (Wikipathways):WP236 |
| 1.43343932289745e-09 | 6.33394346217144e-07 | 6 | 24 | Triacylglyceride Synthesis (Wikipathways):WP325 |
| 0.000889394642292785 | 0.0312770449206296 | 3 | 39 | Vitamin A and carotenoid metabolism (Wikipathways):WP716 |
| 0.000622138261174885 | 0.0262542346215801 | 4 | 80 | Opioid Signalling (Reactome):REACT_15295 |
| 1.20965097703998e-05 | 0.00127618178077717 | 9 | 289 | Metabolism of lipids and lipoproteins (Reactome):REACT_22258 |
| 0.000767963155434517 | 0.0303825423368781 | 8 | 401 | Transmembrane transport of small molecules (Reactome):REACT_15518 |
| 3.34962726576139e-05 | 0.0026503925740337 | 6 | 125 | Integration of energy metabolism (Reactome):REACT_1505 |
| 0.000116253226851286 | 0.00566063789206646 | 5 | 98 | EGFR1 down reg. targets (Netpath):NetPath_4 |
| 3.17560479078695e-06 | 0.000502539458142035 | 15 | 740 | TGF beta receptor down reg. targets (Netpath):NetPath_7 |
| 0.000823880409676361 | 0.0306774293720668 | 3 | 38 | Notch down reg. targets (Netpath):NetPath_3 |
| 4.41162345535417e-05 | 0.00310284183026576 | 5 | 80 | IL-6 up reg. targets (Netpath):NetPath_18 |
| 0.000368380941343833 | 0.0166560811336176 | 3 | 29 | {PRKACA,33} (Static Module):NA |
| 0.000109539480310196 | 0.00566063789206646 | 4 | 51 | {RXRA,51} (Static Module):NA |
Enriched Gene Ontology terms on this co-expression cluster<b>Summary:</b> Results for GOStat analysis on co-expressed clusters. Each cluster with promoters mapping to at least two different genes was analysed with GOStat (PMID: 14962934) with default parameter. <br><b>Analyst:</b> Erik Arner<br><br>link to source dataset<br>data
| GO ID | GO name | FDR corrected p-value |
|---|---|---|
| GO:0032502 | developmental process | 1.44758351806356e-08 |
| GO:0048869 | cellular developmental process | 1.55801439970252e-07 |
| GO:0030154 | cell differentiation | 1.55801439970252e-07 |
| GO:0032501 | multicellular organismal process | 0.00013888712459945 |
| GO:0006629 | lipid metabolic process | 0.000235056696877894 |
| GO:0009892 | negative regulation of metabolic process | 0.000576597647610056 |
| GO:0032787 | monocarboxylic acid metabolic process | 0.00122729074302504 |
| GO:0005737 | cytoplasm | 0.00190713505058476 |
| GO:0008219 | cell death | 0.00190713505058476 |
| GO:0016265 | death | 0.00190713505058476 |
| GO:0048468 | cell development | 0.00276798902360524 |
| GO:0044464 | cell part | 0.0047208105991819 |
| GO:0031324 | negative regulation of cellular metabolic process | 0.0047208105991819 |
| GO:0016020 | membrane | 0.0047208105991819 |
| GO:0048519 | negative regulation of biological process | 0.0047208105991819 |
| GO:0006094 | gluconeogenesis | 0.00618644275660867 |
| GO:0048731 | system development | 0.00631000422900511 |
| GO:0019752 | carboxylic acid metabolic process | 0.00631000422900511 |
| GO:0006082 | organic acid metabolic process | 0.00631000422900511 |
| GO:0007275 | multicellular organismal development | 0.00631000422900511 |
| GO:0006090 | pyruvate metabolic process | 0.00741278280740494 |
| GO:0048523 | negative regulation of cellular process | 0.00844746972301368 |
| GO:0048856 | anatomical structure development | 0.00890410491531604 |
| GO:0065007 | biological regulation | 0.00890410491531604 |
| GO:0044425 | membrane part | 0.0105626186113451 |
| GO:0008374 | O-acyltransferase activity | 0.0105626186113451 |
| GO:0050789 | regulation of biological process | 0.0114146378907499 |
| GO:0019319 | hexose biosynthetic process | 0.0115851242472725 |
| GO:0046364 | monosaccharide biosynthetic process | 0.0117099348707802 |
| GO:0046165 | alcohol biosynthetic process | 0.0117099348707802 |
| GO:0048518 | positive regulation of biological process | 0.0120136234488833 |
| GO:0044255 | cellular lipid metabolic process | 0.0121345569480361 |
| GO:0004860 | protein kinase inhibitor activity | 0.0121345569480361 |
| GO:0007160 | cell-matrix adhesion | 0.0121345569480361 |
| GO:0046870 | cadmium ion binding | 0.0121345569480361 |
| GO:0022603 | regulation of anatomical structure morphogenesis | 0.0121345569480361 |
| GO:0008360 | regulation of cell shape | 0.0121345569480361 |
| GO:0022604 | regulation of cell morphogenesis | 0.0121345569480361 |
| GO:0019210 | kinase inhibitor activity | 0.0121345569480361 |
| GO:0031589 | cell-substrate adhesion | 0.0130649615122204 |
| GO:0048522 | positive regulation of cellular process | 0.013700175333045 |
| GO:0042551 | neuron maturation | 0.0140208936446501 |
| GO:0016481 | negative regulation of transcription | 0.0141283785389882 |
| GO:0006631 | fatty acid metabolic process | 0.0141283785389882 |
| GO:0006006 | glucose metabolic process | 0.0141448961742067 |
| GO:0045892 | negative regulation of transcription, DNA-dependent | 0.017789450268002 |
| GO:0006915 | apoptosis | 0.0193947418019869 |
| GO:0012501 | programmed cell death | 0.0195148584824532 |
| GO:0042981 | regulation of apoptosis | 0.0195148584824532 |
| GO:0006917 | induction of apoptosis | 0.0195148584824532 |
| GO:0045934 | negative regulation of nucleobase, nucleoside, nucleotide and nucleic acid metabolic process | 0.0195148584824532 |
| GO:0012502 | induction of programmed cell death | 0.0195183692068321 |
| GO:0043067 | regulation of programmed cell death | 0.0195890639989346 |
| GO:0006066 | alcohol metabolic process | 0.0197206795668438 |
| GO:0016021 | integral to membrane | 0.0197606032506796 |
| GO:0000122 | negative regulation of transcription from RNA polymerase II promoter | 0.0204639850561413 |
| GO:0031224 | intrinsic to membrane | 0.0213303297091542 |
| GO:0051179 | localization | 0.0219566588181505 |
| GO:0004861 | cyclin-dependent protein kinase inhibitor activity | 0.0227151728494451 |
| GO:0000267 | cell fraction | 0.0227151728494451 |
| GO:0042593 | glucose homeostasis | 0.023962948630332 |
| GO:0019835 | cytolysis | 0.023962948630332 |
| GO:0016411 | acylglycerol O-acyltransferase activity | 0.023962948630332 |
| GO:0033500 | carbohydrate homeostasis | 0.023962948630332 |
| GO:0016051 | carbohydrate biosynthetic process | 0.023962948630332 |
| GO:0050793 | regulation of developmental process | 0.0242222990816159 |
| GO:0045859 | regulation of protein kinase activity | 0.0243083846020063 |
| GO:0043549 | regulation of kinase activity | 0.0262481043471013 |
| GO:0016042 | lipid catabolic process | 0.0271219040623413 |
| GO:0051338 | regulation of transferase activity | 0.0271219040623413 |
| GO:0007193 | G-protein signaling, adenylate cyclase inhibiting pathway | 0.0271219040623413 |
| GO:0015459 | potassium channel regulator activity | 0.0271219040623413 |
| GO:0044262 | cellular carbohydrate metabolic process | 0.0271219040623413 |
| GO:0017015 | regulation of transforming growth factor beta receptor signaling pathway | 0.0292325917701192 |
| GO:0051017 | actin filament bundle formation | 0.0292325917701192 |
| GO:0043065 | positive regulation of apoptosis | 0.0297751733614886 |
| GO:0007243 | protein kinase cascade | 0.0297751733614886 |
| GO:0043068 | positive regulation of programmed cell death | 0.0302453078878655 |
| GO:0005887 | integral to plasma membrane | 0.032657335975714 |
| GO:0019318 | hexose metabolic process | 0.0351199912068023 |
| GO:0031226 | intrinsic to plasma membrane | 0.0351199912068023 |
| GO:0005996 | monosaccharide metabolic process | 0.037291172313484 |
| GO:0005741 | mitochondrial outer membrane | 0.0375118298510018 |
| GO:0005515 | protein binding | 0.0375118298510018 |
| GO:0007188 | G-protein signaling, coupled to cAMP nucleotide second messenger | 0.0375118298510018 |
| GO:0016044 | membrane organization and biogenesis | 0.0375118298510018 |
| GO:0044424 | intracellular part | 0.0375118298510018 |
| GO:0030395 | lactose binding | 0.0375118298510018 |
| GO:0030581 | intracellular protein transport in host | 0.0375118298510018 |
| GO:0005477 | pyruvate secondary active transmembrane transporter activity | 0.0375118298510018 |
| GO:0004903 | growth hormone receptor activity | 0.0375118298510018 |
| GO:0051708 | intracellular protein transport in other organism during symbiotic interaction | 0.0375118298510018 |
| GO:0043540 | 6-phosphofructo-2-kinase/fructose-2,6-biphosphatase 1 complex | 0.0375118298510018 |
| GO:0006848 | pyruvate transport | 0.0375118298510018 |
| GO:0016815 | hydrolase activity, acting on carbon-nitrogen (but not peptide) bonds, in nitriles | 0.0375118298510018 |
| GO:0000257 | nitrilase activity | 0.0375118298510018 |
| GO:0004782 | sulfinoalanine decarboxylase activity | 0.0375118298510018 |
| GO:0015168 | glycerol transmembrane transporter activity | 0.0375118298510018 |
| GO:0015254 | glycerol channel activity | 0.0375118298510018 |
| GO:0019060 | intracellular transport of viral proteins in host cell | 0.0375118298510018 |
| GO:0045163 | clustering of voltage-gated potassium channels | 0.0375118298510018 |
| GO:0048030 | disaccharide binding | 0.0375118298510018 |
| GO:0050833 | pyruvate transmembrane transporter activity | 0.0375118298510018 |
| GO:0019933 | cAMP-mediated signaling | 0.0375118298510018 |
| GO:0006357 | regulation of transcription from RNA polymerase II promoter | 0.0390104825047872 |
| GO:0031968 | organelle outer membrane | 0.0439685200703348 |
| GO:0051234 | establishment of localization | 0.0439685200703348 |
| GO:0019216 | regulation of lipid metabolic process | 0.0439685200703348 |
| GO:0019867 | outer membrane | 0.0467401766928364 |
| GO:0005319 | lipid transporter activity | 0.0467401766928364 |
| GO:0015758 | glucose transport | 0.0490088369011223 |
| GO:0010324 | membrane invagination | 0.0496171881746509 |
| GO:0006897 | endocytosis | 0.0496171881746509 |
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>cell_data<br>uberon_data<br><br>
| Ontology term | p-value | n |
|---|---|---|
| fat cell | 4.43e-34 | 15 |
| adipocyte of omentum tissue | 7.92e-12 | 3 |
| Ontology term | p-value | n |
|---|---|---|
| valve | 7.92e-12 | 3 |
| cardiac mesenchyme | 7.92e-12 | 3 |
| cardial valve | 7.92e-12 | 3 |
| tunica intima | 7.92e-12 | 3 |
| heart layer | 7.92e-12 | 3 |
| endocardium | 7.92e-12 | 3 |
| endocardial cushion | 7.92e-12 | 3 |
| presumptive endocardium | 7.92e-12 | 3 |
| pulmonary valve | 1.43e-09 | 1 |
| semi-lunar valve | 1.43e-09 | 1 |
| adult organism | 1.61e-09 | 114 |
| mitral valve | 1.99e-09 | 1 |
| vermiform appendix | 2.16e-09 | 1 |
| caecum | 2.16e-09 | 1 |
| midgut | 2.16e-09 | 1 |
Overrepresented TFBS (DNA) motifs on this co-expression cluster<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}}} |
ENCODE TF ChIP-seq peak enrichment analysis<b>Summary:</b> For each TF and each co-expression cluster, the number of promoters with ENCODE TF ChIP signal was compared with the rest of promoters from the robust set using Fisher's exact test. Clusters with significant ChIP enrichment (q <= 0.05) after Benjamini-Hochberg correction were retained. <br><b>Analyst:</b> Erik Arner<br><br>link to source dataset<br><br>data
(#promoters = Number of promoters in this coexpression cluster that have ChIP signal of the TF)
| TF | #promoters | Enrichment | p-value | q-value |
|---|---|---|---|---|
| STAT3#6774 | 86 | 1.45445979060332 | 0.000306297982836585 | 0.00315914033472942 |
| ZNF274#10782 | 4 | 9.14306208261192 | 0.00103201747672837 | 0.00729988982404569 |
Relative expression of the co-expression cluster<b>Summary:</b>Co-expression clusters are compared against FANTOM5 samples to obtain relative expression. <br><b>Analyst:</b>NA<br><br>link to data source<br> data
