MCL coexpression mm9:222: Difference between revisions
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{{MCL_coexpression_mm9 | 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metabolic process;0.000579663125793403;22589,109331,81702,21969,94246!GO:0005694;chromosome;0.00116694694797247;22589,109331,21969,94246!GO:0006261;DNA-dependent DNA replication;0.00897090187905303;81702,21969!GO:0043231;intracellular membrane-bound organelle;0.00917410638940051;22589,20658,109331,81702,21969,100710,11737,228005,94246!GO:0043227;membrane-bound organelle;0.00917410638940051;22589,20658,109331,81702,21969,100710,11737,228005,94246!GO:0043229;intracellular organelle;0.0171860332599524;22589,20658,109331,81702,21969,100710,11737,228005,94246!GO:0043226;organelle;0.0171860332599524;22589,20658,109331,81702,21969,100710,11737,228005,94246!GO:0003682;chromatin binding;0.0171860332599524;22589,94246!GO:0003676;nucleic acid binding;0.0171860332599524;22589,20658,67039,81702,21969,94246!GO:0043204;perikaryon;0.0185730418610017;21969!GO:0003677;DNA binding;0.0185730418610017;22589,20658,81702,21969,94246!GO:0006139;nucleobase, nucleoside, nucleotide and nucleic acid metabolic process;0.0198003208463124;22589,109331,67039,81702,21969,94246!GO:0003917;DNA topoisomerase type I activity;0.0200732190252243;21969!GO:0006260;DNA replication;0.0200732190252243;81702,21969!GO:0003918;DNA topoisomerase (ATP-hydrolyzing) activity;0.0222346756453473;21969!GO:0016853;isomerase activity;0.0226901522085912;21969,228005!GO:0040016;embryonic cleavage;0.0237111410404715;21969!GO:0003916;DNA topoisomerase activity;0.0246049051280258;21969!GO:0006281;DNA repair;0.0246049051280258;22589,81702!GO:0000785;chromatin;0.0246049051280258;22589,94246!GO:0006265;DNA topological change;0.0246049051280258;21969!GO:0030983;mismatched DNA binding;0.0246049051280258;81702!GO:0032392;DNA geometric change;0.0246049051280258;21969!GO:0006268;DNA unwinding during replication;0.0246049051280258;21969!GO:0032508;DNA duplex unwinding;0.0246049051280258;21969!GO:0043232;intracellular non-membrane-bound organelle;0.026948408889325;22589,109331,21969,94246!GO:0043228;non-membrane-bound organelle;0.026948408889325;22589,109331,21969,94246!GO:0006298;mismatch repair;0.026948408889325;81702!GO:0045005;maintenance of fidelity during DNA-dependent DNA replication;0.0279557744820937;81702!GO:0006974;response to DNA damage stimulus;0.0279557744820937;22589,81702!GO:0051301;cell division;0.0279557744820937;21969,100710!GO:0044424;intracellular part;0.029801112072005;22589,20658,109331,81702,21969,100710,11737,228005,94246!GO:0009719;response to endogenous stimulus;0.0299004299360272;22589,81702!GO:0016363;nuclear matrix;0.0304182013251265;11737!GO:0005622;intracellular;0.0305396399708874;22589,20658,109331,81702,21969,100710,11737,228005,94246!GO:0006325;establishment and/or maintenance of chromatin architecture;0.0305396399708874;109331,94246!GO:0043170;macromolecule metabolic process;0.0305396399708874;22589,109331,67039,81702,21969,228005,94246!GO:0007492;endoderm development;0.0305396399708874;81702!GO:0006323;DNA packaging;0.0305396399708874;109331,94246!GO:0043283;biopolymer metabolic process;0.0343721912992878;22589,109331,67039,81702,21969,94246!GO:0044427;chromosomal part;0.0343721912992878;22589,94246!GO:0003690;double-stranded DNA binding;0.0346113957404018;81702!GO:0003725;double-stranded RNA binding;0.0418267428160646;20658!GO:0051276;chromosome organization and 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|coexpression_dpi_cluster_scores_median=-0.131667287129191,-0.180274689346406,-0.180274689346406,-0.178101321237085,-0.188314225435835,-0.17208118264908,-0.178101321237085,-0.0969814055909249,-0.0448944763101239,-0.0589712542050569,-0.0240982272923006,-0.0298794156505872,-0.109850899433735,-0.0862633603332607,-0.0760338213386094,-0.0316870528290055,0.0341181482083817,-0.0639158829728916,-0.0655923102739395,-0.178482233814886,-0.0513213176617718,-0.0994336053156176,-0.0946371933100123,-0.0761782420959494,-0.170746144160095,-0.181539686342046,-0.186624607472909,-0.178101321237085,-0.178101321237085,-0.178734914532133,-0.181539686342046,-0.186624607472909,-0.180274689346406,-0.193893011938994,-0.180274689346406,-0.17208118264908,-0.180274689346406,-0.14866777359524,-0.181539686342046,-0.169656096896275,-0.149700657682213,-0.161023467221053,-0.140366672932388,-0.0745484433550502,-0.0817525223528981,0.0543638794631033,-0.188314225435835,-0.180274689346406,-0.180274689346406,-0.178101321237085,-0.180274689346406,-0.188314225435835,-0.0666914861468412,-0.100783889465809,0.0923311061877717,0,-0.115432414129512,-0.0817525223528981,-0.108295432381344,-0.0222659739980148,-0.115432414129512,-0.188314225435835,-0.188314225435835,-0.179348086785112,-0.186624607472909,-0.193893011938994,-0.186624607472909,-0.181539686342046,0.065217923790187,-0.0458928753520424,-0.0669591266356784,-0.169656096896275,-0.149700657682213,-0.0851117569985141,-0.0903414435386857,-0.125665098325543,-0.100783889465809,0.180008369060768,0.221323094439138,-0.104462008572722,-0.062765065907747,0.00483452562463099,-0.122880392252717,-0.0927359537809747,0.195797871080633,0.193302040190839,0.178842904540122,-0.041741166914385,-0.137954353313828,-0.127184903148412,-0.100783889465809,-0.178101321237085,-0.178101321237085,0.00716232067362027,-0.0254759278881926,-0.0144890116618507,-0.0927359537809747,0.0263036941969779,0.0560561868470508,0.0664149161164216,-0.137859425097703,-0.179348086785112,-0.17208118264908,-0.193893011938994,0.00335639251384019,0.0163232614514831,-0.000413509745104207,-0.0803702482299161,-0.0817525223528981,-0.0809917865194563,-0.00634037431328718,0.0505214327821639,-0.0494139402790497,0.148196956382418,0.254953521135658,-0.0150689639484846,-0.0194980642655981,-0.111002599327235,-0.149700657682213,0.0884677855288994,0.230352629487737,0.0631276931124197,-0.178482233814886,0.150306122394376,0.0613903384296543,-0.0268632367166008,-0.112441925220423,-0.186624607472909,-0.117705119377144,0.0471067497359626,0.0481763289246949,0.202379091376542,0.000724552194647982,0.176124077582384,0.0581972644601979,0.104769526199305,0.240554529747975,-0.0403609128631094,-0.0327902109486945,0.024226417473255,0.312842044221725,-0.149700657682213,-0.0371675572618865,0.331251301875758,0.207410018640199,0.332248110520626,0.132214059671188,0.306134256339595,-0.0880700555997119,0.0597987978803275,0.00528019198822996,-0.0734064302875209,0.323505473660712,-0.0561135882283813,-0.000483676823335874,0.0727997892461091,-0.180274689346406,-0.178101321237085,-0.122663206137667,-0.0121560065966144,0.289795216722919,0.205699151678129,0.0559051117222742,0.231279665208818,0.362266112520122,0.380444345393444,0.106572827308056,0.241385523097723,0.205540393868481,0.417799977180417,0.0573936722991921,0.00491735427244411,0.133439623670164,-0.0238063472137411,-0.0338736210324545,0.267496896229626,-0.0821425676136806,-0.0817525223528981,0.280797141565519,0.334526005248336,-0.0519410693991096,-0.000642214049809159,0.0336563175486626,-0.0891852287756878,0.108285104114955,0.0501368351292811,0.205436468791729,0.0534082864264137,0.117426291446769,0.185747708399722,0.334704730815594,0.0635537278075118,-0.170746144160095,0.272127663640427,0.035443622531248,0.365244215247819,0.318416022393452,0.353252497098733,0.154699609160742,0.267378820245493,0.240895210896849,-0.0219449804937289,-0.136477656043278,-0.0120680038408329,-0.0499051113555247,0.094565245756465,-0.0714078872566744,-0.0927908324112148,-0.125665098325543,-0.0768112144781404,0.240523467957724,0.195914340179016,0.984965162167238,0.0622342768898974,0.115932257742053,0.051916922483933,-0.0698115460245994,-0.00429852637857631,0.0341718335342421,-0.169656096896275,0.0604221256385643,0.224244286332003,0.346160824894279,0.0247014474852917,0,0.307658166304024,0.172404707144594,0.413633364770909,0.317894025449795,0.346988842648646,0.302786421402947,0.121644402431552,0.0121931185131915,0.141589936649239,-0.0146140236230657,-0.120850618036594,-0.0477778485252909,-0.0176643072891535,-0.0399799828754249,-0.0961253582789558,-0.0836864796544587,-0.0927359537809747,0.130836350352697,-0.00099852375081555,0.0487539262952288,-0.0927359537809747,-0.00208285070571368,0.101329308568412,-0.00349510778316064,0.0392559190165875,-0.0611316056832238,-0.0492379762618084,0.147876204126668,0.0334522133496647,-0.170746144160095,0.106399399755749,0.0272782181059079,0.206725955281205,-0.150526661879793,-0.0817525223528981,-0.0498721837402962,0.04056211406082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| |||
|gostat_on_MCL_coexpression=GO:0005634;nucleus;0.000579663125793403;22589,20658,109331,81702,21969,100710,11737,228005,94246!GO:0006259;DNA metabolic process;0.000579663125793403;22589,109331,81702,21969,94246!GO:0005694;chromosome;0.00116694694797247;22589,109331,21969,94246!GO:0006261;DNA-dependent DNA replication;0.00897090187905303;81702,21969!GO:0043231;intracellular membrane-bound organelle;0.00917410638940051;22589,20658,109331,81702,21969,100710,11737,228005,94246!GO:0043227;membrane-bound organelle;0.00917410638940051;22589,20658,109331,81702,21969,100710,11737,228005,94246!GO:0043229;intracellular organelle;0.0171860332599524;22589,20658,109331,81702,21969,100710,11737,228005,94246!GO:0043226;organelle;0.0171860332599524;22589,20658,109331,81702,21969,100710,11737,228005,94246!GO:0003682;chromatin binding;0.0171860332599524;22589,94246!GO:0003676;nucleic acid binding;0.0171860332599524;22589,20658,67039,81702,21969,94246!GO:0043204;perikaryon;0.0185730418610017;21969!GO:0003677;DNA binding;0.0185730418610017;22589,20658,81702,21969,94246!GO:0006139;nucleobase, nucleoside, nucleotide and nucleic acid metabolic process;0.0198003208463124;22589,109331,67039,81702,21969,94246!GO:0003917;DNA topoisomerase type I activity;0.0200732190252243;21969!GO:0006260;DNA replication;0.0200732190252243;81702,21969!GO:0003918;DNA topoisomerase (ATP-hydrolyzing) activity;0.0222346756453473;21969!GO:0016853;isomerase activity;0.0226901522085912;21969,228005!GO:0040016;embryonic cleavage;0.0237111410404715;21969!GO:0003916;DNA topoisomerase activity;0.0246049051280258;21969!GO:0006281;DNA repair;0.0246049051280258;22589,81702!GO:0000785;chromatin;0.0246049051280258;22589,94246!GO:0006265;DNA topological change;0.0246049051280258;21969!GO:0030983;mismatched DNA binding;0.0246049051280258;81702!GO:0032392;DNA geometric change;0.0246049051280258;21969!GO:0006268;DNA unwinding during replication;0.0246049051280258;21969!GO:0032508;DNA duplex unwinding;0.0246049051280258;21969!GO:0043232;intracellular non-membrane-bound organelle;0.026948408889325;22589,109331,21969,94246!GO:0043228;non-membrane-bound organelle;0.026948408889325;22589,109331,21969,94246!GO:0006298;mismatch repair;0.026948408889325;81702!GO:0045005;maintenance of fidelity during DNA-dependent DNA replication;0.0279557744820937;81702!GO:0006974;response to DNA damage stimulus;0.0279557744820937;22589,81702!GO:0051301;cell division;0.0279557744820937;21969,100710!GO:0044424;intracellular part;0.029801112072005;22589,20658,109331,81702,21969,100710,11737,228005,94246!GO:0009719;response to endogenous stimulus;0.0299004299360272;22589,81702!GO:0016363;nuclear matrix;0.0304182013251265;11737!GO:0005622;intracellular;0.0305396399708874;22589,20658,109331,81702,21969,100710,11737,228005,94246!GO:0006325;establishment and/or maintenance of chromatin architecture;0.0305396399708874;109331,94246!GO:0043170;macromolecule metabolic process;0.0305396399708874;22589,109331,67039,81702,21969,228005,94246!GO:0007492;endoderm development;0.0305396399708874;81702!GO:0006323;DNA packaging;0.0305396399708874;109331,94246!GO:0043283;biopolymer metabolic process;0.0343721912992878;22589,109331,67039,81702,21969,94246!GO:0044427;chromosomal part;0.0343721912992878;22589,94246!GO:0003690;double-stranded DNA binding;0.0346113957404018;81702!GO:0003725;double-stranded RNA binding;0.0418267428160646;20658!GO:0051276;chromosome organization and biogenesis;0.0498164078999933;109331,94246! | |||
|ontology_enrichment_celltype= | |||
|ontology_enrichment_disease= | |||
|ontology_enrichment_uberon=UBERON:0000922!6.00e-08!320;UBERON:0000468!1.50e-07!333;UBERON:0001048!6.05e-07!134;UBERON:0002021!7.94e-07!10;UBERON:0000411!7.94e-07!10;UBERON:0001950!7.94e-07!10 | |||
}} |
Latest revision as of 14:55, 17 September 2013
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
GO ID | GO name | FDR corrected p-value |
---|---|---|
GO:0005634 | nucleus | 0.000579663125793403 |
GO:0006259 | DNA metabolic process | 0.000579663125793403 |
GO:0005694 | chromosome | 0.00116694694797247 |
GO:0006261 | DNA-dependent DNA replication | 0.00897090187905303 |
GO:0043231 | intracellular membrane-bound organelle | 0.00917410638940051 |
GO:0043227 | membrane-bound organelle | 0.00917410638940051 |
GO:0043229 | intracellular organelle | 0.0171860332599524 |
GO:0043226 | organelle | 0.0171860332599524 |
GO:0003682 | chromatin binding | 0.0171860332599524 |
GO:0003676 | nucleic acid binding | 0.0171860332599524 |
GO:0043204 | perikaryon | 0.0185730418610017 |
GO:0003677 | DNA binding | 0.0185730418610017 |
GO:0006139 | nucleobase, nucleoside, nucleotide and nucleic acid metabolic process | 0.0198003208463124 |
GO:0003917 | DNA topoisomerase type I activity | 0.0200732190252243 |
GO:0006260 | DNA replication | 0.0200732190252243 |
GO:0003918 | DNA topoisomerase (ATP-hydrolyzing) activity | 0.0222346756453473 |
GO:0016853 | isomerase activity | 0.0226901522085912 |
GO:0040016 | embryonic cleavage | 0.0237111410404715 |
GO:0003916 | DNA topoisomerase activity | 0.0246049051280258 |
GO:0006281 | DNA repair | 0.0246049051280258 |
GO:0000785 | chromatin | 0.0246049051280258 |
GO:0006265 | DNA topological change | 0.0246049051280258 |
GO:0030983 | mismatched DNA binding | 0.0246049051280258 |
GO:0032392 | DNA geometric change | 0.0246049051280258 |
GO:0006268 | DNA unwinding during replication | 0.0246049051280258 |
GO:0032508 | DNA duplex unwinding | 0.0246049051280258 |
GO:0043232 | intracellular non-membrane-bound organelle | 0.026948408889325 |
GO:0043228 | non-membrane-bound organelle | 0.026948408889325 |
GO:0006298 | mismatch repair | 0.026948408889325 |
GO:0045005 | maintenance of fidelity during DNA-dependent DNA replication | 0.0279557744820937 |
GO:0006974 | response to DNA damage stimulus | 0.0279557744820937 |
GO:0051301 | cell division | 0.0279557744820937 |
GO:0044424 | intracellular part | 0.029801112072005 |
GO:0009719 | response to endogenous stimulus | 0.0299004299360272 |
GO:0016363 | nuclear matrix | 0.0304182013251265 |
GO:0005622 | intracellular | 0.0305396399708874 |
GO:0006325 | establishment and/or maintenance of chromatin architecture | 0.0305396399708874 |
GO:0043170 | macromolecule metabolic process | 0.0305396399708874 |
GO:0007492 | endoderm development | 0.0305396399708874 |
GO:0006323 | DNA packaging | 0.0305396399708874 |
GO:0043283 | biopolymer metabolic process | 0.0343721912992878 |
GO:0044427 | chromosomal part | 0.0343721912992878 |
GO:0003690 | double-stranded DNA binding | 0.0346113957404018 |
GO:0003725 | double-stranded RNA binding | 0.0418267428160646 |
GO:0051276 | chromosome organization and biogenesis | 0.0498164078999933 |
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 |
---|---|---|
embryo | 6.00e-08 | 320 |
multi-cellular organism | 1.50e-07 | 333 |
primordium | 6.05e-07 | 134 |
occipital lobe | 7.94e-07 | 10 |
visual cortex | 7.94e-07 | 10 |
neocortex | 7.94e-07 | 10 |
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 | 1.97127e-10 |
MA0004.1 | 0.184728 |
MA0006.1 | 0.142703 |
MA0007.1 | 0.384663 |
MA0009.1 | 0.295418 |
MA0014.1 | 2.4938e-07 |
MA0017.1 | 0.176909 |
MA0019.1 | 0.511584 |
MA0024.1 | 0.263595 |
MA0025.1 | 0.48174 |
MA0027.1 | 1.83212 |
MA0028.1 | 0.0579302 |
MA0029.1 | 1.2835 |
MA0030.1 | 1.30072 |
MA0031.1 | 0.228273 |
MA0038.1 | 0.109925 |
MA0040.1 | 0.822451 |
MA0041.1 | 1.62057 |
MA0042.1 | 0.773378 |
MA0043.1 | 0.369607 |
MA0046.1 | 0.32239 |
MA0048.1 | 0.00186738 |
MA0050.1 | 0.489958 |
MA0051.1 | 0.114454 |
MA0052.1 | 0.836068 |
MA0055.1 | 0.0187927 |
MA0056.1 | 0 |
MA0057.1 | 0.00600452 |
MA0058.1 | 0.0230527 |
MA0059.1 | 0.264983 |
MA0060.1 | 0.019438 |
MA0061.1 | 0.0293946 |
MA0063.1 | 0 |
MA0066.1 | 0.340713 |
MA0067.1 | 0.577859 |
MA0068.1 | 0.00148638 |
MA0069.1 | 0.31103 |
MA0070.1 | 0.820264 |
MA0071.1 | 1.27426 |
MA0072.1 | 1.46446 |
MA0073.1 | 8.32938e-13 |
MA0074.1 | 0.614782 |
MA0076.1 | 0.0175818 |
MA0077.1 | 0.281511 |
MA0078.1 | 0.817761 |
MA0081.1 | 0.880688 |
MA0083.1 | 0.368979 |
MA0084.1 | 0.878418 |
MA0087.1 | 0.891033 |
MA0088.1 | 0.0364594 |
MA0089.1 | 0 |
MA0090.1 | 0.151401 |
MA0091.1 | 0.43862 |
MA0092.1 | 0.151694 |
MA0093.1 | 0.0627068 |
MA0095.1 | 0 |
MA0098.1 | 0 |
MA0100.1 | 0.0824768 |
MA0101.1 | 0.116255 |
MA0103.1 | 0.191785 |
MA0105.1 | 0.0049716 |
MA0106.1 | 0.136153 |
MA0107.1 | 0.183235 |
MA0108.2 | 0.185867 |
MA0109.1 | 0 |
MA0111.1 | 0.164809 |
MA0113.1 | 0.76969 |
MA0114.1 | 0.338492 |
MA0115.1 | 0.971884 |
MA0116.1 | 0.010499 |
MA0117.1 | 0.346488 |
MA0119.1 | 0.116736 |
MA0122.1 | 0.362012 |
MA0124.1 | 1.31617 |
MA0125.1 | 0.468049 |
MA0130.1 | 0 |
MA0131.1 | 0.168986 |
MA0132.1 | 0 |
MA0133.1 | 0 |
MA0135.1 | 3.72634 |
MA0136.1 | 0.320131 |
MA0139.1 | 0.00178035 |
MA0140.1 | 0.589362 |
MA0141.1 | 0.689449 |
MA0142.1 | 1.82729 |
MA0143.1 | 0.80811 |
MA0144.1 | 0.0886256 |
MA0145.1 | 0.000418296 |
MA0146.1 | 7.60916e-06 |
MA0147.1 | 0.0345488 |
MA0148.1 | 0.775803 |
MA0149.1 | 0.0292146 |
MA0062.2 | 0.00559468 |
MA0035.2 | 1.00811 |
MA0039.2 | 2.468e-12 |
MA0138.2 | 0.164211 |
MA0002.2 | 0.516387 |
MA0137.2 | 0.019155 |
MA0104.2 | 0.0156277 |
MA0047.2 | 0.354114 |
MA0112.2 | 0.0457301 |
MA0065.2 | 0.238153 |
MA0150.1 | 0.169655 |
MA0151.1 | 0 |
MA0152.1 | 1.18244 |
MA0153.1 | 1.06037 |
MA0154.1 | 0.000201169 |
MA0155.1 | 0.00355102 |
MA0156.1 | 0.202379 |
MA0157.1 | 0.197497 |
MA0158.1 | 0 |
MA0159.1 | 0.111377 |
MA0160.1 | 0.450634 |
MA0161.1 | 0 |
MA0162.1 | 1.92674e-05 |
MA0163.1 | 1.39118e-06 |
MA0164.1 | 0.0969555 |
MA0080.2 | 0.0708729 |
MA0018.2 | 0.101591 |
MA0099.2 | 0.16046 |
MA0079.2 | 0 |
MA0102.2 | 0.928086 |
MA0258.1 | 0.719571 |
MA0259.1 | 0.00546925 |
MA0442.1 | 0 |