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MCL coexpression mm9:249: Difference between revisions

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{{MCL_coexpression_mm9|gostat_on_MCL_coexpression=GO:0043565;sequence-specific DNA binding;4.66219642927358e-10;107751,110796,15417,15416,15414,231044,27140,15415!GO:0003700;transcription factor activity;3.58983629733356e-08;107751,110796,15417,15416,15414,231044,27140,15415!GO:0006355;regulation of transcription, DNA-dependent;8.15457988534263e-06;107751,110796,15417,15416,15414,231044,27140,15415!GO:0006351;transcription, DNA-dependent;8.15457988534263e-06;107751,110796,15417,15416,15414,231044,27140,15415!GO:0032774;RNA biosynthetic process;8.15457988534263e-06;107751,110796,15417,15416,15414,231044,27140,15415!GO:0003677;DNA binding;8.15457988534263e-06;107751,110796,15417,15416,15414,231044,27140,15415!GO:0045449;regulation of transcription;8.15457988534263e-06;107751,110796,15417,15416,15414,231044,27140,15415!GO:0019219;regulation of nucleobase, nucleoside, nucleotide and nucleic acid metabolic process;8.17833195692428e-06;107751,110796,15417,15416,15414,231044,27140,15415!GO:0006350;transcription;8.17833195692428e-06;107751,110796,15417,15416,15414,231044,27140,15415!GO:0010468;regulation of gene expression;9.52377099101757e-06;107751,110796,15417,15416,15414,231044,27140,15415!GO:0031323;regulation of cellular metabolic process;1.18398879549564e-05;107751,110796,15417,15416,15414,231044,27140,15415!GO:0019222;regulation of metabolic process;1.35026510106574e-05;107751,110796,15417,15416,15414,231044,27140,15415!GO:0005667;transcription factor complex;1.35026510106574e-05;15414,231044,15417,15416,15415!GO:0016070;RNA metabolic process;1.51097115166252e-05;107751,110796,15417,15416,15414,231044,27140,15415!GO:0044451;nucleoplasm part;3.49430956486395e-05;15414,231044,15417,15416,15415!GO:0007389;pattern specification process;3.87818823351528e-05;15414,15417,15416,15415!GO:0005654;nucleoplasm;3.87818823351528e-05;15414,231044,15417,15416,15415!GO:0010467;gene expression;4.71955645572212e-05;107751,110796,15417,15416,15414,231044,27140,15415!GO:0003676;nucleic acid binding;5.37328013617935e-05;107751,110796,15417,15416,15414,231044,27140,15415!GO:0031981;nuclear lumen;7.65794779702869e-05;15414,231044,15417,15416,15415!GO:0006139;nucleobase, nucleoside, nucleotide and nucleic acid metabolic process;8.64219204453706e-05;107751,110796,15417,15416,15414,231044,27140,15415!GO:0031974;membrane-enclosed lumen;0.000119410850917134;15414,231044,15417,15416,15415!GO:0043233;organelle lumen;0.000119410850917134;15414,231044,15417,15416,15415!GO:0050794;regulation of cellular process;0.000128489435236984;107751,110796,15417,15416,15414,231044,27140,15415!GO:0007275;multicellular organismal development;0.000128489435236984;107751,15414,110796,15417,27140,15416,15415!GO:0050789;regulation of biological process;0.000271072154718551;107751,110796,15417,15416,15414,231044,27140,15415!GO:0048731;system development;0.000362869330720921;107751,15414,15417,27140,15416,15415!GO:0044428;nuclear part;0.000385792860398734;15414,231044,15417,15416,15415!GO:0009887;organ morphogenesis;0.000438275391251869;15414,15417,15416,15415!GO:0065007;biological regulation;0.000489557220292832;107751,110796,15417,15416,15414,231044,27140,15415!GO:0005634;nucleus;0.000553179326799751;107751,110796,15417,15416,15414,231044,27140,15415!GO:0032502;developmental process;0.000610335707727658;107751,15414,110796,15417,27140,15416,15415!GO:0009653;anatomical structure morphogenesis;0.000610335707727658;107751,15414,15417,15416,15415!GO:0043283;biopolymer metabolic process;0.000634737226865075;107751,110796,15417,15416,15414,231044,27140,15415!GO:0048856;anatomical structure development;0.000666403870768045;107751,15414,15417,27140,15416,15415!GO:0001764;neuron migration;0.00138249730469124;107751,27140!GO:0043234;protein complex;0.00268018557224522;15414,231044,15417,15416,15415!GO:0043170;macromolecule metabolic process;0.00430030132281161;107751,110796,15417,15416,15414,231044,27140,15415!GO:0032501;multicellular organismal process;0.00462409006547361;107751,15414,110796,15417,27140,15416,15415!GO:0032991;macromolecular complex;0.00713615806975326;15414,231044,15417,15416,15415!GO:0048665;neuron fate specification;0.00840996362120453;27140!GO:0016048;detection of temperature stimulus;0.00984924320142664;107751!GO:0044238;primary metabolic process;0.0107087141513915;107751,110796,15417,15416,15414,231044,27140,15415!GO:0044237;cellular metabolic process;0.0107487238965365;107751,110796,15417,15416,15414,231044,27140,15415!GO:0043231;intracellular membrane-bound organelle;0.010792233213583;107751,110796,15417,15416,15414,231044,27140,15415!GO:0043227;membrane-bound organelle;0.010792233213583;107751,110796,15417,15416,15414,231044,27140,15415!GO:0048513;organ development;0.0108488712215354;15414,15417,15416,15415!GO:0044446;intracellular organelle part;0.0117221798027382;15414,231044,15417,15416,15415!GO:0044422;organelle part;0.0117221798027382;15414,231044,15417,15416,15415!GO:0045665;negative regulation of neuron differentiation;0.0220079944178839;27140!GO:0016477;cell migration;0.0228919786313328;107751,27140!GO:0030182;neuron differentiation;0.0230886866595075;107751,27140!GO:0005184;neuropeptide hormone activity;0.0241807241083434;54615!GO:0007585;respiratory gaseous exchange;0.0241807241083434;27140!GO:0048663;neuron fate commitment;0.0257588656760298;27140!GO:0009593;detection of chemical stimulus;0.0257588656760298;107751!GO:0048699;generation of neurons;0.0269494900472055;107751,27140!GO:0001708;cell fate specification;0.0270170432208276;27140!GO:0051674;localization of cell;0.0270170432208276;107751,27140!GO:0006928;cell motility;0.0270170432208276;107751,27140!GO:0022008;neurogenesis;0.0288057512136958;107751,27140!GO:0045664;regulation of neuron differentiation;0.0298693434670383;27140!GO:0043229;intracellular organelle;0.0337707392262282;107751,110796,15417,15416,15414,231044,27140,15415!GO:0043226;organelle;0.0337707392262282;107751,110796,15417,15416,15414,231044,27140,15415!GO:0009582;detection of abiotic stimulus;0.0462354691560304;107751!GO:0009266;response to temperature stimulus;0.0475812774093105;107751!GO:0009581;detection of external stimulus;0.0488849198894495;107751!}}
{{MCL_coexpression_mm9
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|gostat_on_MCL_coexpression=GO:0043565;sequence-specific DNA binding;4.66219642927358e-10;107751,110796,15417,15416,15414,231044,27140,15415!GO:0003700;transcription factor activity;3.58983629733356e-08;107751,110796,15417,15416,15414,231044,27140,15415!GO:0006355;regulation of transcription, DNA-dependent;8.15457988534263e-06;107751,110796,15417,15416,15414,231044,27140,15415!GO:0006351;transcription, DNA-dependent;8.15457988534263e-06;107751,110796,15417,15416,15414,231044,27140,15415!GO:0032774;RNA biosynthetic process;8.15457988534263e-06;107751,110796,15417,15416,15414,231044,27140,15415!GO:0003677;DNA binding;8.15457988534263e-06;107751,110796,15417,15416,15414,231044,27140,15415!GO:0045449;regulation of transcription;8.15457988534263e-06;107751,110796,15417,15416,15414,231044,27140,15415!GO:0019219;regulation of nucleobase, nucleoside, nucleotide and nucleic acid metabolic process;8.17833195692428e-06;107751,110796,15417,15416,15414,231044,27140,15415!GO:0006350;transcription;8.17833195692428e-06;107751,110796,15417,15416,15414,231044,27140,15415!GO:0010468;regulation of gene expression;9.52377099101757e-06;107751,110796,15417,15416,15414,231044,27140,15415!GO:0031323;regulation of cellular metabolic process;1.18398879549564e-05;107751,110796,15417,15416,15414,231044,27140,15415!GO:0019222;regulation of metabolic process;1.35026510106574e-05;107751,110796,15417,15416,15414,231044,27140,15415!GO:0005667;transcription factor complex;1.35026510106574e-05;15414,231044,15417,15416,15415!GO:0016070;RNA metabolic process;1.51097115166252e-05;107751,110796,15417,15416,15414,231044,27140,15415!GO:0044451;nucleoplasm part;3.49430956486395e-05;15414,231044,15417,15416,15415!GO:0007389;pattern specification process;3.87818823351528e-05;15414,15417,15416,15415!GO:0005654;nucleoplasm;3.87818823351528e-05;15414,231044,15417,15416,15415!GO:0010467;gene expression;4.71955645572212e-05;107751,110796,15417,15416,15414,231044,27140,15415!GO:0003676;nucleic acid binding;5.37328013617935e-05;107751,110796,15417,15416,15414,231044,27140,15415!GO:0031981;nuclear lumen;7.65794779702869e-05;15414,231044,15417,15416,15415!GO:0006139;nucleobase, nucleoside, nucleotide and nucleic acid metabolic process;8.64219204453706e-05;107751,110796,15417,15416,15414,231044,27140,15415!GO:0031974;membrane-enclosed lumen;0.000119410850917134;15414,231044,15417,15416,15415!GO:0043233;organelle lumen;0.000119410850917134;15414,231044,15417,15416,15415!GO:0050794;regulation of cellular process;0.000128489435236984;107751,110796,15417,15416,15414,231044,27140,15415!GO:0007275;multicellular organismal development;0.000128489435236984;107751,15414,110796,15417,27140,15416,15415!GO:0050789;regulation of biological process;0.000271072154718551;107751,110796,15417,15416,15414,231044,27140,15415!GO:0048731;system development;0.000362869330720921;107751,15414,15417,27140,15416,15415!GO:0044428;nuclear part;0.000385792860398734;15414,231044,15417,15416,15415!GO:0009887;organ morphogenesis;0.000438275391251869;15414,15417,15416,15415!GO:0065007;biological regulation;0.000489557220292832;107751,110796,15417,15416,15414,231044,27140,15415!GO:0005634;nucleus;0.000553179326799751;107751,110796,15417,15416,15414,231044,27140,15415!GO:0032502;developmental process;0.000610335707727658;107751,15414,110796,15417,27140,15416,15415!GO:0009653;anatomical structure morphogenesis;0.000610335707727658;107751,15414,15417,15416,15415!GO:0043283;biopolymer metabolic process;0.000634737226865075;107751,110796,15417,15416,15414,231044,27140,15415!GO:0048856;anatomical structure development;0.000666403870768045;107751,15414,15417,27140,15416,15415!GO:0001764;neuron migration;0.00138249730469124;107751,27140!GO:0043234;protein complex;0.00268018557224522;15414,231044,15417,15416,15415!GO:0043170;macromolecule metabolic process;0.00430030132281161;107751,110796,15417,15416,15414,231044,27140,15415!GO:0032501;multicellular organismal process;0.00462409006547361;107751,15414,110796,15417,27140,15416,15415!GO:0032991;macromolecular complex;0.00713615806975326;15414,231044,15417,15416,15415!GO:0048665;neuron fate specification;0.00840996362120453;27140!GO:0016048;detection of temperature stimulus;0.00984924320142664;107751!GO:0044238;primary metabolic process;0.0107087141513915;107751,110796,15417,15416,15414,231044,27140,15415!GO:0044237;cellular metabolic process;0.0107487238965365;107751,110796,15417,15416,15414,231044,27140,15415!GO:0043231;intracellular membrane-bound organelle;0.010792233213583;107751,110796,15417,15416,15414,231044,27140,15415!GO:0043227;membrane-bound organelle;0.010792233213583;107751,110796,15417,15416,15414,231044,27140,15415!GO:0048513;organ development;0.0108488712215354;15414,15417,15416,15415!GO:0044446;intracellular organelle part;0.0117221798027382;15414,231044,15417,15416,15415!GO:0044422;organelle part;0.0117221798027382;15414,231044,15417,15416,15415!GO:0045665;negative regulation of neuron differentiation;0.0220079944178839;27140!GO:0016477;cell migration;0.0228919786313328;107751,27140!GO:0030182;neuron differentiation;0.0230886866595075;107751,27140!GO:0005184;neuropeptide hormone activity;0.0241807241083434;54615!GO:0007585;respiratory gaseous exchange;0.0241807241083434;27140!GO:0048663;neuron fate commitment;0.0257588656760298;27140!GO:0009593;detection of chemical stimulus;0.0257588656760298;107751!GO:0048699;generation of neurons;0.0269494900472055;107751,27140!GO:0001708;cell fate specification;0.0270170432208276;27140!GO:0051674;localization of cell;0.0270170432208276;107751,27140!GO:0006928;cell motility;0.0270170432208276;107751,27140!GO:0022008;neurogenesis;0.0288057512136958;107751,27140!GO:0045664;regulation of neuron differentiation;0.0298693434670383;27140!GO:0043229;intracellular organelle;0.0337707392262282;107751,110796,15417,15416,15414,231044,27140,15415!GO:0043226;organelle;0.0337707392262282;107751,110796,15417,15416,15414,231044,27140,15415!GO:0009582;detection of abiotic stimulus;0.0462354691560304;107751!GO:0009266;response to temperature stimulus;0.0475812774093105;107751!GO:0009581;detection of external stimulus;0.0488849198894495;107751!
}}

Revision as of 11:05, 11 October 2012


Phase1 CAGE Peaks

 Short description
Mm9::chr11:33103551..33103561,-p4@Tlx3
Mm9::chr11:33103563..33103583,-p1@Tlx3
Mm9::chr11:33103589..33103599,-p3@Tlx3
Mm9::chr11:33103600..33103611,-p2@Tlx3
Mm9::chr11:96132456..96132467,+p4@Hoxb9
Mm9::chr11:96132523..96132538,+p3@Hoxb9
Mm9::chr11:96132544..96132553,+p6@Hoxb9
Mm9::chr11:96132930..96132971,+p@chr11:96132930..96132971
+
Mm9::chr11:96143545..96143556,+p6@Hoxb8
Mm9::chr11:96143666..96143725,+p1@Hoxb8
Mm9::chr11:96143728..96143745,+p4@Hoxb8
Mm9::chr11:96143843..96143868,+p3@Hoxb8
Mm9::chr11:96143962..96144035,+p2@Hoxb8
Mm9::chr11:96144050..96144065,+p5@Hoxb8
Mm9::chr11:96144282..96144308,+p@chr11:96144282..96144308
+
Mm9::chr11:96144337..96144354,+p@chr11:96144337..96144354
+
Mm9::chr11:96145362..96145389,+p4@Hoxb7
Mm9::chr11:96145537..96145556,+p6@Hoxb7
Mm9::chr11:96146086..96146100,+p@chr11:96146086..96146100
+
Mm9::chr11:96148092..96148105,+p@chr11:96148092..96148105
+
Mm9::chr11:96153467..96153473,+p10@Hoxb6
Mm9::chr11:96160098..96160112,+p8@Hoxb6
Mm9::chr11:96160119..96160135,+p7@Hoxb6
Mm9::chr11:96608388..96608420,+p@chr11:96608388..96608420
+
Mm9::chr14:33412570..33412586,+p1@Prrxl1
Mm9::chr14:33413108..33413118,+p3@Prrxl1
Mm9::chr15:102355046..102355050,-p1@Npff
Mm9::chr15:102802660..102802666,+p@chr15:102802660..102802666
+
Mm9::chr18:84255362..84255383,-p@chr18:84255362..84255383
-
Mm9::chr2:135877916..135877935,+p7@6330527O06Rik
Mm9::chr2:70399563..70399583,+p@chr2:70399563..70399583
+
Mm9::chr2:74550015..74550057,+p2@Hoxd3
Mm9::chr2:74555045..74555052,+p@chr2:74555045..74555052
+
Mm9::chr5:24032551..24032557,-p1@Gbx1


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 IDGO nameFDR corrected p-value
GO:0043565sequence-specific DNA binding4.66219642927358e-10
GO:0003700transcription factor activity3.58983629733356e-08
GO:0006355regulation of transcription, DNA-dependent8.15457988534263e-06
GO:0006351transcription, DNA-dependent8.15457988534263e-06
GO:0032774RNA biosynthetic process8.15457988534263e-06
GO:0003677DNA binding8.15457988534263e-06
GO:0045449regulation of transcription8.15457988534263e-06
GO:0019219regulation of nucleobase, nucleoside, nucleotide and nucleic acid metabolic process8.17833195692428e-06
GO:0006350transcription8.17833195692428e-06
GO:0010468regulation of gene expression9.52377099101757e-06
GO:0031323regulation of cellular metabolic process1.18398879549564e-05
GO:0019222regulation of metabolic process1.35026510106574e-05
GO:0005667transcription factor complex1.35026510106574e-05
GO:0016070RNA metabolic process1.51097115166252e-05
GO:0044451nucleoplasm part3.49430956486395e-05
GO:0007389pattern specification process3.87818823351528e-05
GO:0005654nucleoplasm3.87818823351528e-05
GO:0010467gene expression4.71955645572212e-05
GO:0003676nucleic acid binding5.37328013617935e-05
GO:0031981nuclear lumen7.65794779702869e-05
GO:0006139nucleobase, nucleoside, nucleotide and nucleic acid metabolic process8.64219204453706e-05
GO:0031974membrane-enclosed lumen0.000119410850917134
GO:0043233organelle lumen0.000119410850917134
GO:0050794regulation of cellular process0.000128489435236984
GO:0007275multicellular organismal development0.000128489435236984
GO:0050789regulation of biological process0.000271072154718551
GO:0048731system development0.000362869330720921
GO:0044428nuclear part0.000385792860398734
GO:0009887organ morphogenesis0.000438275391251869
GO:0065007biological regulation0.000489557220292832
GO:0005634nucleus0.000553179326799751
GO:0032502developmental process0.000610335707727658
GO:0009653anatomical structure morphogenesis0.000610335707727658
GO:0043283biopolymer metabolic process0.000634737226865075
GO:0048856anatomical structure development0.000666403870768045
GO:0001764neuron migration0.00138249730469124
GO:0043234protein complex0.00268018557224522
GO:0043170macromolecule metabolic process0.00430030132281161
GO:0032501multicellular organismal process0.00462409006547361
GO:0032991macromolecular complex0.00713615806975326
GO:0048665neuron fate specification0.00840996362120453
GO:0016048detection of temperature stimulus0.00984924320142664
GO:0044238primary metabolic process0.0107087141513915
GO:0044237cellular metabolic process0.0107487238965365
GO:0043231intracellular membrane-bound organelle0.010792233213583
GO:0043227membrane-bound organelle0.010792233213583
GO:0048513organ development0.0108488712215354
GO:0044446intracellular organelle part0.0117221798027382
GO:0044422organelle part0.0117221798027382
GO:0045665negative regulation of neuron differentiation0.0220079944178839
GO:0016477cell migration0.0228919786313328
GO:0030182neuron differentiation0.0230886866595075
GO:0005184neuropeptide hormone activity0.0241807241083434
GO:0007585respiratory gaseous exchange0.0241807241083434
GO:0048663neuron fate commitment0.0257588656760298
GO:0009593detection of chemical stimulus0.0257588656760298
GO:0048699generation of neurons0.0269494900472055
GO:0001708cell fate specification0.0270170432208276
GO:0051674localization of cell0.0270170432208276
GO:0006928cell motility0.0270170432208276
GO:0022008neurogenesis0.0288057512136958
GO:0045664regulation of neuron differentiation0.0298693434670383
GO:0043229intracellular organelle0.0337707392262282
GO:0043226organelle0.0337707392262282
GO:0009582detection of abiotic stimulus0.0462354691560304
GO:0009266response to temperature stimulus0.0475812774093105
GO:0009581detection of external stimulus0.0488849198894495



Relative expression of the co-expression cluster over median <br>Analyst:


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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>disease_data<br>

Cell Type
Ontology termp-valuen

Uber Anatomy
Ontology termp-valuen

Disease
Ontology termp-valuen


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}}}

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