MCL coexpression mm9:779: Difference between revisions
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{{MCL_coexpression_mm9| | 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transport;0.0103893245423907;103988!GO:0046323;glucose import;0.0103893245423907;68938!GO:0046324;regulation of glucose import;0.0103893245423907;68938!GO:0046835;carbohydrate phosphorylation;0.0103893245423907;103988!GO:0009898;internal side of plasma membrane;0.0103893245423907;68938!GO:0004396;hexokinase activity;0.0103893245423907;103988!GO:0000300;peripheral to membrane of membrane fraction;0.0103893245423907;68938!GO:0050796;regulation of insulin secretion;0.0181738477443164;103988!GO:0043269;regulation of ion transport;0.0189624563800178;103988!GO:0009620;response to fungus;0.0196850987954215;84506!GO:0006739;NADP metabolic process;0.0203496909631566;103988!GO:0005624;membrane fraction;0.0220875780328587;13097,68938!GO:0046883;regulation of hormone secretion;0.0269043085221581;103988!GO:0006769;nicotinamide metabolic process;0.0272316569735245;103988!GO:0030073;insulin secretion;0.0272316569735245;103988!GO:0019362;pyridine nucleotide metabolic 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| ||
Latest revision as of 15:52, 17 September 2013
Phase1 CAGE Peaks
| Short description | |
|---|---|
| Mm9::chr11:120538639..120538669,+ | p11@Aspscr1 |
| Mm9::chr11:5815129..5815144,- | p1@Gck |
| Mm9::chr12:73729838..73729853,- | p@chr12:73729838..73729853 - |
| Mm9::chr12:73729855..73729874,- | p@chr12:73729855..73729874 - |
| Mm9::chr12:73729883..73729894,- | p@chr12:73729883..73729894 - |
| Mm9::chr12:73729916..73729925,- | p@chr12:73729916..73729925 - |
| Mm9::chr12:73729943..73729952,- | p@chr12:73729943..73729952 - |
| Mm9::chr19:39537557..39537571,- | p1@Cyp2c38 |
| Mm9::chr7:31729038..31729054,- | p1@Hamp |
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:0048878 | chemical homeostasis | 0.000751951602892798 |
| GO:0042593 | glucose homeostasis | 0.000751951602892798 |
| GO:0033500 | carbohydrate homeostasis | 0.000751951602892798 |
| GO:0042592 | homeostatic process | 0.000907847436039409 |
| GO:0000267 | cell fraction | 0.00259532194131859 |
| GO:0051049 | regulation of transport | 0.00343572495553038 |
| GO:0065008 | regulation of biological quality | 0.00343572495553038 |
| GO:0004340 | glucokinase activity | 0.00404195352970897 |
| GO:0032024 | positive regulation of insulin secretion | 0.00404195352970897 |
| GO:0005792 | microsome | 0.00658136694942709 |
| GO:0042598 | vesicular fraction | 0.00658136694942709 |
| GO:0050832 | defense response to fungus | 0.00909290069114756 |
| GO:0019725 | cellular homeostasis | 0.0100350514033023 |
| GO:0001678 | cell glucose homeostasis | 0.0103893245423907 |
| GO:0043266 | regulation of potassium ion transport | 0.0103893245423907 |
| GO:0046323 | glucose import | 0.0103893245423907 |
| GO:0046324 | regulation of glucose import | 0.0103893245423907 |
| GO:0046835 | carbohydrate phosphorylation | 0.0103893245423907 |
| GO:0009898 | internal side of plasma membrane | 0.0103893245423907 |
| GO:0004396 | hexokinase activity | 0.0103893245423907 |
| GO:0000300 | peripheral to membrane of membrane fraction | 0.0103893245423907 |
| GO:0050796 | regulation of insulin secretion | 0.0181738477443164 |
| GO:0043269 | regulation of ion transport | 0.0189624563800178 |
| GO:0009620 | response to fungus | 0.0196850987954215 |
| GO:0006739 | NADP metabolic process | 0.0203496909631566 |
| GO:0005624 | membrane fraction | 0.0220875780328587 |
| GO:0046883 | regulation of hormone secretion | 0.0269043085221581 |
| GO:0006769 | nicotinamide metabolic process | 0.0272316569735245 |
| GO:0030073 | insulin secretion | 0.0272316569735245 |
| GO:0019362 | pyridine nucleotide metabolic process | 0.0272316569735245 |
| GO:0055072 | iron ion homeostasis | 0.0272316569735245 |
| GO:0006879 | cellular iron ion homeostasis | 0.0272316569735245 |
| GO:0015758 | glucose transport | 0.0276980184414035 |
| GO:0008645 | hexose transport | 0.0276980184414035 |
| GO:0030072 | peptide hormone secretion | 0.0276980184414035 |
| GO:0015749 | monosaccharide transport | 0.0276980184414035 |
| GO:0002790 | peptide secretion | 0.0276980184414035 |
| GO:0019200 | carbohydrate kinase activity | 0.0276980184414035 |
| GO:0006733 | oxidoreduction coenzyme metabolic process | 0.0290280042862062 |
| GO:0050381 | unspecific monooxygenase activity | 0.0290280042862062 |
| GO:0048471 | perinuclear region of cytoplasm | 0.0309673661411862 |
| GO:0015833 | peptide transport | 0.0320500055687079 |
| GO:0016712 | oxidoreductase activity, acting on paired donors, with incorporation or reduction of molecular oxygen, reduced flavin or flavoprotein as one donor, and incorporation of one atom of oxygen | 0.0320500055687079 |
| GO:0006767 | water-soluble vitamin metabolic process | 0.0321432061621352 |
| GO:0046879 | hormone secretion | 0.0330352193800603 |
| GO:0006096 | glycolysis | 0.0354582835388274 |
| GO:0051046 | regulation of secretion | 0.0382632967523427 |
| GO:0006007 | glucose catabolic process | 0.0382632967523427 |
| GO:0046365 | monosaccharide catabolic process | 0.0382632967523427 |
| GO:0019320 | hexose catabolic process | 0.0382632967523427 |
| GO:0005625 | soluble fraction | 0.0382632967523427 |
| GO:0012506 | vesicle membrane | 0.0382632967523427 |
| GO:0046164 | alcohol catabolic process | 0.0382632967523427 |
| GO:0008643 | carbohydrate transport | 0.0408023295041978 |
| GO:0006766 | vitamin metabolic process | 0.0408023295041978 |
| GO:0044275 | cellular carbohydrate catabolic process | 0.0426450879325889 |
| GO:0019898 | extrinsic to membrane | 0.0437905296077511 |
| GO:0016052 | carbohydrate catabolic process | 0.0448955523849472 |
| GO:0044444 | cytoplasmic part | 0.0462388432671752 |
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>cell_data<br>uberon_data<br><br>
| Ontology term | p-value | n |
|---|---|---|
| metabolising cell | 3.82e-26 | 5 |
| endopolyploid cell | 3.82e-26 | 5 |
| parenchymal cell | 3.82e-26 | 5 |
| polyploid cell | 3.82e-26 | 5 |
| hepatocyte | 3.82e-26 | 5 |
| fibroblast | 3.65e-09 | 1 |
| hepatic stellate cell | 3.65e-09 | 1 |
| endodermal cell | 8.99e-07 | 20 |
| Ontology term | p-value | n |
|---|---|---|
| liver | 9.03e-23 | 22 |
| epithelial sac | 9.03e-23 | 22 |
| digestive gland | 9.03e-23 | 22 |
| epithelium of foregut-midgut junction | 9.03e-23 | 22 |
| anatomical boundary | 9.03e-23 | 22 |
| hepatobiliary system | 9.03e-23 | 22 |
| foregut-midgut junction | 9.03e-23 | 22 |
| hepatic diverticulum | 9.03e-23 | 22 |
| liver primordium | 9.03e-23 | 22 |
| septum transversum | 9.03e-23 | 22 |
| liver bud | 9.03e-23 | 22 |
| digestive tract diverticulum | 9.16e-22 | 23 |
| sac | 9.16e-22 | 23 |
| exocrine gland | 5.41e-20 | 25 |
| exocrine system | 5.41e-20 | 25 |
| trunk mesenchyme | 9.74e-14 | 45 |
| abdomen element | 1.44e-12 | 49 |
| abdominal segment element | 1.44e-12 | 49 |
| abdominal segment of trunk | 1.44e-12 | 49 |
| abdomen | 1.44e-12 | 49 |
| epithelial tube | 2.06e-10 | 47 |
| endocrine gland | 3.82e-10 | 60 |
| mesenchyme | 5.75e-10 | 61 |
| entire embryonic mesenchyme | 5.75e-10 | 61 |
| gland | 2.60e-09 | 65 |
| subdivision of trunk | 3.69e-09 | 66 |
| gut epithelium | 8.15e-09 | 55 |
| endocrine system | 2.45e-08 | 72 |
| trunk region element | 1.56e-07 | 79 |
| unilaminar epithelium | 3.03e-07 | 66 |
| endo-epithelium | 6.67e-07 | 69 |
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 | 0.00143485 |
| MA0004.1 | 0.394951 |
| MA0006.1 | 0.238555 |
| MA0007.1 | 2.64186 |
| MA0009.1 | 0.82278 |
| MA0014.1 | 0.00813637 |
| MA0017.1 | 0.726051 |
| MA0019.1 | 0.642876 |
| MA0024.1 | 0.779446 |
| MA0025.1 | 1.05446 |
| MA0027.1 | 2.46647 |
| MA0028.1 | 0.24786 |
| MA0029.1 | 0.757957 |
| MA0030.1 | 1.80346 |
| MA0031.1 | 0.729293 |
| MA0038.1 | 0.534262 |
| MA0040.1 | 0.835181 |
| MA0041.1 | 4.24392 |
| MA0042.1 | 3.19033 |
| MA0043.1 | 0.918718 |
| MA0046.1 | 0.858391 |
| MA0048.1 | 0.281053 |
| MA0050.1 | 0.431976 |
| MA0051.1 | 0.542972 |
| MA0052.1 | 0.84317 |
| MA0055.1 | 0.692644 |
| MA0056.1 | 0 |
| MA0057.1 | 0.0745664 |
| MA0058.1 | 1.49242 |
| MA0059.1 | 1.53319 |
| MA0060.1 | 0.169058 |
| MA0061.1 | 0.194456 |
| MA0063.1 | 0 |
| MA0066.1 | 0.523573 |
| MA0067.1 | 1.16502 |
| MA0068.1 | 0.077274 |
| MA0069.1 | 0.843506 |
| MA0070.1 | 0.833895 |
| MA0071.1 | 0.431174 |
| MA0072.1 | 0.825495 |
| MA0073.1 | 0.0431817 |
| MA0074.1 | 0.488775 |
| MA0076.1 | 0.279739 |
| MA0077.1 | 0.804033 |
| MA0078.1 | 0.575205 |
| MA0081.1 | 0.338098 |
| MA0083.1 | 0.917931 |
| MA0084.1 | 1.49188 |
| MA0087.1 | 0.87515 |
| MA0088.1 | 0.413524 |
| MA0089.1 | 0 |
| MA0090.1 | 0.362551 |
| MA0091.1 | 0.407455 |
| MA0092.1 | 0.362847 |
| MA0093.1 | 0.709711 |
| MA0095.1 | 0 |
| MA0098.1 | 0 |
| MA0100.1 | 0.477594 |
| MA0101.1 | 0.324888 |
| MA0103.1 | 0.272167 |
| MA0105.1 | 0.109964 |
| MA0106.1 | 0.582805 |
| MA0107.1 | 0.266586 |
| MA0108.2 | 0.665343 |
| MA0109.1 | 0 |
| MA0111.1 | 0.375908 |
| MA0113.1 | 0.555251 |
| MA0114.1 | 0.19245 |
| MA0115.1 | 0.921497 |
| MA0116.1 | 0.238371 |
| MA0117.1 | 0.88947 |
| MA0119.1 | 0.325434 |
| MA0122.1 | 2.10074 |
| MA0124.1 | 4.08836 |
| MA0125.1 | 1.03833 |
| MA0130.1 | 0 |
| MA0131.1 | 0.638414 |
| MA0132.1 | 0 |
| MA0133.1 | 0 |
| MA0135.1 | 0.954884 |
| MA0136.1 | 0.508047 |
| MA0139.1 | 0.143341 |
| MA0140.1 | 0.477483 |
| MA0141.1 | 0.29014 |
| MA0142.1 | 0.714976 |
| MA0143.1 | 0.571221 |
| MA0144.1 | 0.195095 |
| MA0145.1 | 0.77191 |
| MA0146.1 | 0.0111657 |
| MA0147.1 | 0.593505 |
| MA0148.1 | 2.78137 |
| MA0149.1 | 0.330018 |
| MA0062.2 | 0.113962 |
| MA0035.2 | 0.482026 |
| MA0039.2 | 0.0946163 |
| MA0138.2 | 0.630612 |
| MA0002.2 | 0.447007 |
| MA0137.2 | 0.287486 |
| MA0104.2 | 0.476119 |
| MA0047.2 | 0.533516 |
| MA0112.2 | 0.200175 |
| MA0065.2 | 0.44341 |
| MA0150.1 | 0.380623 |
| MA0151.1 | 0 |
| MA0152.1 | 0.53362 |
| MA0153.1 | 0.971406 |
| MA0154.1 | 0.0809407 |
| MA0155.1 | 0.0631765 |
| MA0156.1 | 0.278949 |
| MA0157.1 | 0.683365 |
| MA0158.1 | 0 |
| MA0159.1 | 1.15501 |
| MA0160.1 | 0.413266 |
| MA0161.1 | 0 |
| MA0162.1 | 0.0143037 |
| MA0163.1 | 0.0124565 |
| MA0164.1 | 0.508398 |
| MA0080.2 | 0.267388 |
| MA0018.2 | 0.51781 |
| MA0099.2 | 0.624421 |
| MA0079.2 | 6.4867e-05 |
| MA0102.2 | 1.5442 |
| MA0258.1 | 0.180934 |
| MA0259.1 | 0.196451 |
| MA0442.1 | 0 |
