MCL coexpression mm9:1016: Difference between revisions
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{{MCL_coexpression_mm9 | 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structure morphogenesis;0.00296909382281702;11477,14561,14163!GO:0009887;organ morphogenesis;0.00646380487127128;11477,14561!GO:0001655;urogenital system development;0.00646380487127128;11477,14561!GO:0048856;anatomical structure development;0.00646380487127128;11477,14561,14163!GO:0050431;transforming growth factor beta binding;0.00959842217717636;11477!GO:0016361;activin receptor activity, type I;0.0121739696266195;11477!GO:0017002;activin receptor activity;0.0121739696266195;11477!GO:0007507;heart development;0.0121739696266195;11477!GO:0048514;blood vessel morphogenesis;0.0121739696266195;11477!GO:0032502;developmental process;0.0121739696266195;11477,14561,14163!GO:0005025;transforming growth factor beta receptor activity, type I;0.0126221882574342;11477!GO:0001568;blood vessel development;0.0126221882574342;11477!GO:0001944;vasculature development;0.0126221882574342;11477!GO:0048468;cell development;0.0127947411668825;11477,14561!GO:0060037;pharyngeal system development;0.0127947411668825;11477!GO:0050793;regulation of developmental process;0.0157949769515772;14561,14163!GO:0048185;activin binding;0.0169314328740094;11477!GO:0048513;organ development;0.017489293322562;11477,14561!GO:0051145;smooth muscle cell differentiation;0.0215822546795309;11477!GO:0048738;cardiac muscle development;0.0215822546795309;!GO:0004675;transmembrane receptor protein serine/threonine kinase activity;0.0239763413012367;11477!GO:0005024;transforming growth factor beta receptor activity;0.0239763413012367;11477!GO:0048731;system development;0.0242921967687915;11477,14561!GO:0031016;pancreas development;0.0242921967687915;14561!GO:0048869;cellular developmental process;0.0242921967687915;11477,14561!GO:0030154;cell differentiation;0.0242921967687915;11477,14561!GO:0048593;camera-type eye morphogenesis;0.0287550599656491;14561!GO:0022829;wide pore channel activity;0.0287550599656491;!GO:0005243;gap junction channel activity;0.0287550599656491;!GO:0005922;connexon complex;0.0287550599656491;!GO:0001569;patterning of blood vessels;0.0340001801508854;11477!GO:0001755;neural crest cell migration;0.0340268617337679;11477!GO:0001707;mesoderm formation;0.0340268617337679;11477!GO:0048332;mesoderm morphogenesis;0.0340268617337679;11477!GO:0005921;gap junction;0.0340268617337679;!GO:0007275;multicellular organismal development;0.0340268617337679;11477,14561!GO:0001704;formation of primary germ layer;0.0340268617337679;11477!GO:0007281;germ cell development;0.0340268617337679;11477!GO:0001570;vasculogenesis;0.0356044036869571;!GO:0001702;gastrulation with mouth forming second;0.0356241688914495;11477!GO:0014032;neural crest cell development;0.0356241688914495;11477!GO:0014033;neural crest cell differentiation;0.0356241688914495;11477!GO:0001657;ureteric bud development;0.0356241688914495;14561!GO:0007368;determination of left/right symmetry;0.0356390644170355;11477!GO:0001726;ruffle;0.0356390644170355;14163!GO:0009799;determination of 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| |||
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Latest revision as of 16:15, 17 September 2013
Phase1 CAGE Peaks
| Short description | |
|---|---|
| Mm9::chr10:128328730..128328771,- | p1@Gdf11 |
| Mm9::chr11:102680428..102680528,- | p1@Gjc1 |
| Mm9::chr14:52604501..52604531,+ | p2@Arhgef40 |
| Mm9::chr17:28314586..28314627,- | p@chr17:28314586..28314627 - |
| Mm9::chr2:58419568..58419699,- | p1@Acvr1 |
| Mm9::chr9:56842884..56842924,+ | p2@Ptpn9 |
| Mm9::chrX:147481455..147481476,+ | p2@Fgd1 |
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:0009653 | anatomical structure morphogenesis | 0.00296909382281702 |
| GO:0009887 | organ morphogenesis | 0.00646380487127128 |
| GO:0001655 | urogenital system development | 0.00646380487127128 |
| GO:0048856 | anatomical structure development | 0.00646380487127128 |
| GO:0050431 | transforming growth factor beta binding | 0.00959842217717636 |
| GO:0016361 | activin receptor activity, type I | 0.0121739696266195 |
| GO:0017002 | activin receptor activity | 0.0121739696266195 |
| GO:0007507 | heart development | 0.0121739696266195 |
| GO:0048514 | blood vessel morphogenesis | 0.0121739696266195 |
| GO:0032502 | developmental process | 0.0121739696266195 |
| GO:0005025 | transforming growth factor beta receptor activity, type I | 0.0126221882574342 |
| GO:0001568 | blood vessel development | 0.0126221882574342 |
| GO:0001944 | vasculature development | 0.0126221882574342 |
| GO:0048468 | cell development | 0.0127947411668825 |
| GO:0060037 | pharyngeal system development | 0.0127947411668825 |
| GO:0050793 | regulation of developmental process | 0.0157949769515772 |
| GO:0048185 | activin binding | 0.0169314328740094 |
| GO:0048513 | organ development | 0.017489293322562 |
| GO:0051145 | smooth muscle cell differentiation | 0.0215822546795309 |
| GO:0048738 | cardiac muscle development | 0.0215822546795309 |
| GO:0004675 | transmembrane receptor protein serine/threonine kinase activity | 0.0239763413012367 |
| GO:0005024 | transforming growth factor beta receptor activity | 0.0239763413012367 |
| GO:0048731 | system development | 0.0242921967687915 |
| GO:0031016 | pancreas development | 0.0242921967687915 |
| GO:0048869 | cellular developmental process | 0.0242921967687915 |
| GO:0030154 | cell differentiation | 0.0242921967687915 |
| GO:0048593 | camera-type eye morphogenesis | 0.0287550599656491 |
| GO:0022829 | wide pore channel activity | 0.0287550599656491 |
| GO:0005243 | gap junction channel activity | 0.0287550599656491 |
| GO:0005922 | connexon complex | 0.0287550599656491 |
| GO:0001569 | patterning of blood vessels | 0.0340001801508854 |
| GO:0001755 | neural crest cell migration | 0.0340268617337679 |
| GO:0001707 | mesoderm formation | 0.0340268617337679 |
| GO:0048332 | mesoderm morphogenesis | 0.0340268617337679 |
| GO:0005921 | gap junction | 0.0340268617337679 |
| GO:0007275 | multicellular organismal development | 0.0340268617337679 |
| GO:0001704 | formation of primary germ layer | 0.0340268617337679 |
| GO:0007281 | germ cell development | 0.0340268617337679 |
| GO:0001570 | vasculogenesis | 0.0356044036869571 |
| GO:0001702 | gastrulation with mouth forming second | 0.0356241688914495 |
| GO:0014032 | neural crest cell development | 0.0356241688914495 |
| GO:0014033 | neural crest cell differentiation | 0.0356241688914495 |
| GO:0001657 | ureteric bud development | 0.0356241688914495 |
| GO:0007368 | determination of left/right symmetry | 0.0356390644170355 |
| GO:0001726 | ruffle | 0.0356390644170355 |
| GO:0009799 | determination of symmetry | 0.0356390644170355 |
| GO:0009855 | determination of bilateral symmetry | 0.0356390644170355 |
| GO:0048762 | mesenchymal cell differentiation | 0.0380786740322516 |
| GO:0014031 | mesenchymal cell development | 0.0380786740322516 |
| GO:0009880 | embryonic pattern specification | 0.0382708027366175 |
| GO:0048592 | eye morphogenesis | 0.0383992257020482 |
| GO:0014704 | intercalated disc | 0.0383992257020482 |
| GO:0001656 | metanephros development | 0.0383992257020482 |
| GO:0007179 | transforming growth factor beta receptor signaling pathway | 0.0383992257020482 |
| GO:0004702 | receptor signaling protein serine/threonine kinase activity | 0.0383992257020482 |
| GO:0022603 | regulation of anatomical structure morphogenesis | 0.0383992257020482 |
| GO:0022604 | regulation of cell morphogenesis | 0.0383992257020482 |
| GO:0008360 | regulation of cell shape | 0.0383992257020482 |
| GO:0019838 | growth factor binding | 0.0383992257020482 |
| GO:0007498 | mesoderm development | 0.0383992257020482 |
| GO:0030027 | lamellipodium | 0.0383992257020482 |
| GO:0005089 | Rho guanyl-nucleotide exchange factor activity | 0.040850517821372 |
| GO:0035023 | regulation of Rho protein signal transduction | 0.042467210308323 |
| GO:0048754 | branching morphogenesis of a tube | 0.0432895282359754 |
| GO:0005088 | Ras guanyl-nucleotide exchange factor activity | 0.043354858875854 |
| GO:0007369 | gastrulation | 0.0442372284256234 |
| GO:0001763 | morphogenesis of a branching structure | 0.0442372284256234 |
| GO:0042692 | muscle cell differentiation | 0.0442372284256234 |
| GO:0019955 | cytokine binding | 0.0463488678699826 |
| GO:0001822 | kidney development | 0.047693177764072 |
| GO:0019199 | transmembrane receptor protein kinase activity | 0.047693177764072 |
| GO:0048469 | cell maturation | 0.047693177764072 |
| GO:0048729 | tissue morphogenesis | 0.047693177764072 |
| GO:0043010 | camera-type eye development | 0.047693177764072 |
| GO:0031252 | leading edge | 0.047693177764072 |
| GO:0002526 | acute inflammatory response | 0.047693177764072 |
| GO:0045177 | apical part of cell | 0.047693177764072 |
| GO:0007178 | transmembrane receptor protein serine/threonine kinase signaling pathway | 0.0482849740211149 |
| GO:0007266 | Rho protein signal transduction | 0.0482849740211149 |
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 |
|---|---|---|
| ectodermal cell | 6.17e-13 | 44 |
| neurectodermal cell | 6.17e-13 | 44 |
| non-terminally differentiated cell | 7.47e-13 | 49 |
| neural cell | 1.77e-12 | 43 |
| electrically responsive cell | 5.77e-10 | 39 |
| electrically active cell | 5.77e-10 | 39 |
| neuron | 1.25e-09 | 33 |
| neuronal stem cell | 1.25e-09 | 33 |
| neuroblast | 1.25e-09 | 33 |
| electrically signaling cell | 1.25e-09 | 33 |
| Ontology term | p-value | n |
|---|---|---|
| ectoderm-derived structure | 1.30e-08 | 95 |
| ectoderm | 1.30e-08 | 95 |
| presumptive ectoderm | 1.30e-08 | 95 |
| multi-cellular organism | 3.23e-08 | 333 |
| central nervous system | 4.31e-08 | 73 |
| nervous system | 5.55e-08 | 75 |
| embryo | 2.39e-07 | 320 |
| structure with developmental contribution from neural crest | 5.63e-07 | 92 |
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 | 6.59917 |
| MA0004.1 | 0.481116 |
| MA0006.1 | 0.311391 |
| MA0007.1 | 0.465969 |
| MA0009.1 | 0.92425 |
| MA0014.1 | 4.64523 |
| MA0017.1 | 0.337808 |
| MA0019.1 | 0.740036 |
| MA0024.1 | 0.880057 |
| MA0025.1 | 1.15921 |
| MA0027.1 | 2.57545 |
| MA0028.1 | 0.860672 |
| MA0029.1 | 0.858105 |
| MA0030.1 | 0.864739 |
| MA0031.1 | 0.828781 |
| MA0038.1 | 0.62758 |
| MA0040.1 | 0.936879 |
| MA0041.1 | 0.404721 |
| MA0042.1 | 0.391504 |
| MA0043.1 | 1.02178 |
| MA0046.1 | 0.960497 |
| MA0048.1 | 0.801219 |
| MA0050.1 | 0.520357 |
| MA0051.1 | 0.636645 |
| MA0052.1 | 0.945011 |
| MA0055.1 | 0.648475 |
| MA0056.1 | 0 |
| MA0057.1 | 1.80315 |
| MA0058.1 | 0.384683 |
| MA0059.1 | 0.397033 |
| MA0060.1 | 0.656954 |
| MA0061.1 | 2.05557 |
| MA0063.1 | 0 |
| MA0066.1 | 0.616444 |
| MA0067.1 | 1.27078 |
| MA0068.1 | 0.121435 |
| MA0069.1 | 0.945354 |
| MA0070.1 | 0.93557 |
| MA0071.1 | 0.519509 |
| MA0072.1 | 0.927016 |
| MA0073.1 | 0.845602 |
| MA0074.1 | 0.580087 |
| MA0076.1 | 0.356883 |
| MA0077.1 | 0.905143 |
| MA0078.1 | 0.670113 |
| MA0081.1 | 0.420276 |
| MA0083.1 | 1.02098 |
| MA0084.1 | 1.59945 |
| MA0087.1 | 0.977537 |
| MA0088.1 | 2.05511 |
| MA0089.1 | 0 |
| MA0090.1 | 0.446539 |
| MA0091.1 | 0.494398 |
| MA0092.1 | 0.446857 |
| MA0093.1 | 0.329976 |
| MA0095.1 | 0 |
| MA0098.1 | 0 |
| MA0100.1 | 0.568369 |
| MA0101.1 | 0.406019 |
| MA0103.1 | 0.348572 |
| MA0105.1 | 4.5223 |
| MA0106.1 | 1.62423 |
| MA0107.1 | 0.342432 |
| MA0108.2 | 0.763162 |
| MA0109.1 | 0 |
| MA0111.1 | 0.460823 |
| MA0113.1 | 0.649407 |
| MA0114.1 | 0.259463 |
| MA0115.1 | 1.0246 |
| MA0116.1 | 0.836994 |
| MA0117.1 | 0.992087 |
| MA0119.1 | 1.04809 |
| MA0122.1 | 1.01209 |
| MA0124.1 | 1.21735 |
| MA0125.1 | 1.14291 |
| MA0130.1 | 0 |
| MA0131.1 | 0.735438 |
| MA0132.1 | 0 |
| MA0133.1 | 0 |
| MA0135.1 | 1.05845 |
| MA0136.1 | 0.600242 |
| MA0139.1 | 1.7399 |
| MA0140.1 | 0.568252 |
| MA0141.1 | 0.368264 |
| MA0142.1 | 0.814115 |
| MA0143.1 | 0.665982 |
| MA0144.1 | 0.262477 |
| MA0145.1 | 0.631666 |
| MA0146.1 | 2.55638 |
| MA0147.1 | 0.274511 |
| MA0148.1 | 0.49752 |
| MA0149.1 | 0.411562 |
| MA0062.2 | 0.167299 |
| MA0035.2 | 0.573016 |
| MA0039.2 | 3.91294 |
| MA0138.2 | 0.727395 |
| MA0002.2 | 0.592533 |
| MA0137.2 | 0.365364 |
| MA0104.2 | 0.624968 |
| MA0047.2 | 0.626803 |
| MA0112.2 | 0.631649 |
| MA0065.2 | 0.0914071 |
| MA0150.1 | 0.465855 |
| MA0151.1 | 0 |
| MA0152.1 | 0.626912 |
| MA0153.1 | 1.07519 |
| MA0154.1 | 0.792589 |
| MA0155.1 | 3.66586 |
| MA0156.1 | 0.356017 |
| MA0157.1 | 0.781683 |
| MA0158.1 | 0 |
| MA0159.1 | 0.284457 |
| MA0160.1 | 0.50056 |
| MA0161.1 | 0 |
| MA0162.1 | 3.96582 |
| MA0163.1 | 5.14538 |
| MA0164.1 | 0.600609 |
| MA0080.2 | 0.343316 |
| MA0018.2 | 0.610433 |
| MA0099.2 | 0.721008 |
| MA0079.2 | 14.9487 |
| MA0102.2 | 1.65195 |
| MA0258.1 | 0.246285 |
| MA0259.1 | 0.729797 |
| MA0442.1 | 0 |
