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MCL coexpression mm9:262: Difference between revisions

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{{MCL_coexpression_mm9
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specification process;0.000473097416261886;15432,15431,15398,15433!GO:0003700;transcription factor activity;0.00128291389413705;15432,15431,15398,22160,15433!GO:0005667;transcription factor complex;0.00128291389413705;15432,15431,15398,15433!GO:0043565;sequence-specific DNA binding;0.00128291389413705;15432,15431,15398,15433!GO:0009887;organ morphogenesis;0.00147536142509066;15432,15431,15398,15433!GO:0044451;nucleoplasm part;0.00147536142509066;15432,15431,15398,15433!GO:0001501;skeletal development;0.00147536142509066;15432,15431,15433!GO:0009653;anatomical structure morphogenesis;0.00147536142509066;15432,15431,15398,22160,15433!GO:0005654;nucleoplasm;0.00147536142509066;15432,15431,15398,15433!GO:0031981;nuclear lumen;0.00259470647301078;15432,15431,15398,15433!GO:0048513;organ development;0.00266446791328663;15432,15431,15398,22160,15433!GO:0031974;membrane-enclosed lumen;0.00317368745954419;15432,15431,15398,15433!GO:0043233;organelle lumen;0.00317368745954419;15432,15431,15398,15433!GO:0030326;embryonic limb morphogenesis;0.00415540629745191;22160,15433!GO:0035113;embryonic appendage morphogenesis;0.00415540629745191;22160,15433!GO:0048731;system development;0.00489650441409066;15432,15431,15398,22160,15433!GO:0035107;appendage morphogenesis;0.00489650441409066;22160,15433!GO:0035108;limb morphogenesis;0.00489650441409066;22160,15433!GO:0060173;limb development;0.00489650441409066;22160,15433!GO:0048736;appendage development;0.00489650441409066;22160,15433!GO:0044428;nuclear part;0.00551324171480623;15432,15431,15398,15433!GO:0006355;regulation of transcription, DNA-dependent;0.00551324171480623;15432,15431,15398,22160,15433!GO:0006351;transcription, DNA-dependent;0.00551324171480623;15432,15431,15398,22160,15433!GO:0032774;RNA biosynthetic process;0.00551324171480623;15432,15431,15398,22160,15433!GO:0003677;DNA binding;0.00560995379016853;15432,15431,15398,22160,15433!GO:0045449;regulation of transcription;0.00578422189955604;15432,15431,15398,22160,15433!GO:0048856;anatomical structure development;0.00587999880279197;15432,15431,15398,22160,15433!GO:0019219;regulation of nucleobase, nucleoside, nucleotide and nucleic acid metabolic process;0.00587999880279197;15432,15431,15398,22160,15433!GO:0006350;transcription;0.00602887185361421;15432,15431,15398,22160,15433!GO:0010468;regulation of gene expression;0.0067870812496044;15432,15431,15398,22160,15433!GO:0031323;regulation of cellular metabolic process;0.00790017989892396;15432,15431,15398,22160,15433!GO:0007275;multicellular organismal development;0.00849566317085947;15432,15431,15398,22160,15433!GO:0019222;regulation of metabolic process;0.00876372901634206;15432,15431,15398,22160,15433!GO:0016070;RNA metabolic process;0.00958001881999868;15432,15431,15398,22160,15433!GO:0046332;SMAD binding;0.0139741292509268;70673!GO:0045843;negative regulation of striated muscle development;0.0139741292509268;22160!GO:0005518;collagen binding;0.0139741292509268;17534!GO:0048598;embryonic morphogenesis;0.0162956286286687;22160,15433!GO:0043234;protein complex;0.0180532963462087;15432,15431,15398,15433!GO:0010467;gene expression;0.0183035077001981;15432,15431,15398,22160,15433!GO:0003676;nucleic acid binding;0.0198566542060702;15432,15431,15398,22160,15433!GO:0035115;embryonic forelimb morphogenesis;0.0208469733473235;22160!GO:0032502;developmental process;0.0208469733473235;15432,15431,15398,22160,15433!GO:0016202;regulation of striated muscle development;0.0208469733473235;22160!GO:0010092;specification of organ identity;0.0208469733473235;15431!GO:0001759;induction of an organ;0.0208469733473235;15431!GO:0031128;induction;0.0215104325091062;15431!GO:0045168;cell-cell signaling during cell fate commitment;0.0215104325091062;15431!GO:0030246;carbohydrate binding;0.0216351742869658;21930,17534!GO:0035136;forelimb morphogenesis;0.022120169814977;22160!GO:0006139;nucleobase, nucleoside, nucleotide and nucleic acid metabolic process;0.0222185820997572;15432,15431,15398,22160,15433!GO:0005540;hyaluronic acid binding;0.0226823841787019;21930!GO:0050794;regulation of cellular process;0.0290204774403076;15432,15431,15398,22160,15433!GO:0032991;macromolecular complex;0.0299126914371503;15432,15431,15398,15433!GO:0035137;hindlimb morphogenesis;0.0307801926670324;22160!GO:0050789;regulation of biological process;0.043652504504262;15432,15431,15398,22160,15433!GO:0044446;intracellular organelle part;0.0481157019908402;15432,15431,15398,15433!GO:0044422;organelle part;0.0481157019908402;15432,15431,15398,15433!GO:0009790;embryonic 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|gostat_on_MCL_coexpression=GO:0007389;pattern specification process;0.000473097416261886;15432,15431,15398,15433!GO:0003700;transcription factor activity;0.00128291389413705;15432,15431,15398,22160,15433!GO:0005667;transcription factor complex;0.00128291389413705;15432,15431,15398,15433!GO:0043565;sequence-specific DNA binding;0.00128291389413705;15432,15431,15398,15433!GO:0009887;organ morphogenesis;0.00147536142509066;15432,15431,15398,15433!GO:0044451;nucleoplasm part;0.00147536142509066;15432,15431,15398,15433!GO:0001501;skeletal development;0.00147536142509066;15432,15431,15433!GO:0009653;anatomical structure morphogenesis;0.00147536142509066;15432,15431,15398,22160,15433!GO:0005654;nucleoplasm;0.00147536142509066;15432,15431,15398,15433!GO:0031981;nuclear lumen;0.00259470647301078;15432,15431,15398,15433!GO:0048513;organ development;0.00266446791328663;15432,15431,15398,22160,15433!GO:0031974;membrane-enclosed lumen;0.00317368745954419;15432,15431,15398,15433!GO:0043233;organelle lumen;0.00317368745954419;15432,15431,15398,15433!GO:0030326;embryonic limb morphogenesis;0.00415540629745191;22160,15433!GO:0035113;embryonic appendage morphogenesis;0.00415540629745191;22160,15433!GO:0048731;system development;0.00489650441409066;15432,15431,15398,22160,15433!GO:0035107;appendage morphogenesis;0.00489650441409066;22160,15433!GO:0035108;limb morphogenesis;0.00489650441409066;22160,15433!GO:0060173;limb development;0.00489650441409066;22160,15433!GO:0048736;appendage development;0.00489650441409066;22160,15433!GO:0044428;nuclear part;0.00551324171480623;15432,15431,15398,15433!GO:0006355;regulation of transcription, DNA-dependent;0.00551324171480623;15432,15431,15398,22160,15433!GO:0006351;transcription, DNA-dependent;0.00551324171480623;15432,15431,15398,22160,15433!GO:0032774;RNA biosynthetic process;0.00551324171480623;15432,15431,15398,22160,15433!GO:0003677;DNA binding;0.00560995379016853;15432,15431,15398,22160,15433!GO:0045449;regulation of transcription;0.00578422189955604;15432,15431,15398,22160,15433!GO:0048856;anatomical structure development;0.00587999880279197;15432,15431,15398,22160,15433!GO:0019219;regulation of nucleobase, nucleoside, nucleotide and nucleic acid metabolic process;0.00587999880279197;15432,15431,15398,22160,15433!GO:0006350;transcription;0.00602887185361421;15432,15431,15398,22160,15433!GO:0010468;regulation of gene expression;0.0067870812496044;15432,15431,15398,22160,15433!GO:0031323;regulation of cellular metabolic process;0.00790017989892396;15432,15431,15398,22160,15433!GO:0007275;multicellular organismal development;0.00849566317085947;15432,15431,15398,22160,15433!GO:0019222;regulation of metabolic process;0.00876372901634206;15432,15431,15398,22160,15433!GO:0016070;RNA metabolic process;0.00958001881999868;15432,15431,15398,22160,15433!GO:0046332;SMAD binding;0.0139741292509268;70673!GO:0045843;negative regulation of striated muscle development;0.0139741292509268;22160!GO:0005518;collagen binding;0.0139741292509268;17534!GO:0048598;embryonic morphogenesis;0.0162956286286687;22160,15433!GO:0043234;protein complex;0.0180532963462087;15432,15431,15398,15433!GO:0010467;gene expression;0.0183035077001981;15432,15431,15398,22160,15433!GO:0003676;nucleic acid binding;0.0198566542060702;15432,15431,15398,22160,15433!GO:0035115;embryonic forelimb morphogenesis;0.0208469733473235;22160!GO:0032502;developmental process;0.0208469733473235;15432,15431,15398,22160,15433!GO:0016202;regulation of striated muscle development;0.0208469733473235;22160!GO:0010092;specification of organ identity;0.0208469733473235;15431!GO:0001759;induction of an organ;0.0208469733473235;15431!GO:0031128;induction;0.0215104325091062;15431!GO:0045168;cell-cell signaling during cell fate commitment;0.0215104325091062;15431!GO:0030246;carbohydrate binding;0.0216351742869658;21930,17534!GO:0035136;forelimb morphogenesis;0.022120169814977;22160!GO:0006139;nucleobase, nucleoside, nucleotide and nucleic acid metabolic process;0.0222185820997572;15432,15431,15398,22160,15433!GO:0005540;hyaluronic acid binding;0.0226823841787019;21930!GO:0050794;regulation of cellular process;0.0290204774403076;15432,15431,15398,22160,15433!GO:0032991;macromolecular complex;0.0299126914371503;15432,15431,15398,15433!GO:0035137;hindlimb morphogenesis;0.0307801926670324;22160!GO:0050789;regulation of biological process;0.043652504504262;15432,15431,15398,22160,15433!GO:0044446;intracellular organelle part;0.0481157019908402;15432,15431,15398,15433!GO:0044422;organelle part;0.0481157019908402;15432,15431,15398,15433!GO:0009790;embryonic development;0.0488680045372098;22160,15433!
|ontology_enrichment_celltype=
|ontology_enrichment_disease=
|ontology_enrichment_uberon=UBERON:0002102!2.69e-17!7;UBERON:0004710!2.69e-17!7;UBERON:0005419!2.69e-17!7;UBERON:0005417!2.69e-17!7;UBERON:0005729!2.69e-17!7;UBERON:0010708!5.66e-15!8;UBERON:0000026!1.49e-09!12;UBERON:0004708!1.49e-09!12;UBERON:0002101!1.49e-09!12;UBERON:0004357!1.49e-09!12;UBERON:0004347!1.49e-09!12;UBERON:0005732!1.49e-09!12;UBERON:0005733!1.49e-09!12;UBERON:0010707!1.01e-08!13;UBERON:0003102!3.05e-07!22
|tfbs_overrepresentation_for_novel_motifs=0.2121,0.11896,0.410872,0.0755031,0.209326,0.279466,0.401081,0.0859655,1.15057,0.0203364,0.340369,0.121026,1.42371,0.828885,0.23585,0,0.719985,0.197185,0.0717318,0.289816,0.960368,0.15931,0.417302,0.0812711,0.191624,0.150377,0.664883,0.306197,0.28443,0.896068,0.0850386,0.892346,0.625414,0.372412,0.727991,1.04917,0.591572,0.761247,0.149689,0.238943,0.0794914,1.52678,0.131155,0.239128,0.398883,0.248078,0.204367,0.326867,0.020359,0.121216,0.247239,0.166621,0.268737,0.451112,0.465864,0.138517,0.129176,0.739382,0.249356,0.42597,0.320373,0.988345,0.230012,0.239273,0.44515,0.268299,0.584509,0.907487,0.316778,0.768874,0.373674,0.565496,0.0215355,0.494514,0.386747,0.346093,0.0489093,0.196848,1.49968,0.150483,0.360662,0.749016,0.98468,0.176026,0.397678,0.581063,1.3001,2.61058,0.59812,1.06309,0.64713,1.03749,0.34595,0.418991,0.293192,0.00842964,0.331969,0.348163,0.59074,1.26089,0.887589,0.891858,0.436484,0.247661,0.246912,0.294151,0.290513,0.661283,0.15524,0.342885,1.19469,0.437975,0.349606,1.16494,0.653522,0.64149,1.04403,0.95383,0.722152,1.21407,0.499163,0.224692,0.151457,0.196253,0.702969,0.310043,0.818843,0.340627,0.58316,1.41356,0.422342,0.538667,0.556974,0.146415,0.673182,2.02959,0.061587,0.296517,0.628575,1.42304,1.03234,0.588705,0.158669,0.910596,0.242322,0.614954,0.595289,1.38398,0.486947,0.99161,0.670986,0.32218,0.452434,0.129483,0.145874,0.522448,0.500553,0.772485,0.0574053,1.75739,0.637161,0.396979,0.310383,0.201723,0.239991,0.141571,2.55435,0.381906,2.01552
}}

Latest revision as of 14:59, 17 September 2013


Phase1 CAGE Peaks

 Short description
Mm9::chr11:105153425..105153467,+p4@Mrc2
Mm9::chr12:34642510..34642530,+p1@Twist1
Mm9::chr14:56443742..56443756,+p6@Nfatc4
Mm9::chr1:129434016..129434023,-p5@Tmem163
Mm9::chr1:165288513..165288518,+p@chr1:165288513..165288518
+
Mm9::chr2:33574246..33574257,-p3@ENSMUST00000130532
Mm9::chr2:33574267..33574279,-p1@ENSMUST00000130532
Mm9::chr2:33574309..33574319,-p4@ENSMUST00000130532
Mm9::chr2:51893662..51893675,+p2@Tnfaip6
Mm9::chr2:74499251..74499258,-p4@Evx2
Mm9::chr2:74499300..74499309,-p5@Evx2
Mm9::chr2:74506264..74506286,+p1@Hoxd13
Mm9::chr2:74513064..74513089,+p2@Hoxd12
Mm9::chr2:74513125..74513143,+p1@Hoxd12
Mm9::chr2:74513149..74513159,+p@chr2:74513149..74513159
+
Mm9::chr2:74520048..74520064,+p1@Hoxd11
Mm9::chr2:74521516..74521525,+p1@ENSMUST00000136302
Mm9::chr3:29912271..29912291,-p16@Mecom
Mm9::chr3:29912310..29912321,-p23@Mecom
Mm9::chr3:86116124..86116132,+p@chr3:86116124..86116132
+
Mm9::chr4:154011072..154011095,-p6@Prdm16
Mm9::chr4:58566619..58566642,-p9@Lpar1
Mm9::chr5:120246522..120246553,+p@chr5:120246522..120246553
+
Mm9::chr5:120246556..120246565,+p@chr5:120246556..120246565
+
Mm9::chr5:120256413..120256428,-p@chr5:120256413..120256428
-
Mm9::chr6:30660527..30660538,-p@chr6:30660527..30660538
-
Mm9::chr6:52185119..52185126,+p@chr6:52185119..52185126
+
Mm9::chr6:52195000..52195013,+p3@Hoxa11as
Mm9::chr6:52195023..52195038,+p1@Hoxa11as
Mm9::chr6:52210774..52210787,-p1@Hoxa13
Mm9::chr6:52210816..52210831,-p2@Hoxa13
Mm9::chr9:32350571..32350593,-p@chr9:32350571..32350593
-


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:0007389pattern specification process0.000473097416261886
GO:0003700transcription factor activity0.00128291389413705
GO:0005667transcription factor complex0.00128291389413705
GO:0043565sequence-specific DNA binding0.00128291389413705
GO:0009887organ morphogenesis0.00147536142509066
GO:0044451nucleoplasm part0.00147536142509066
GO:0001501skeletal development0.00147536142509066
GO:0009653anatomical structure morphogenesis0.00147536142509066
GO:0005654nucleoplasm0.00147536142509066
GO:0031981nuclear lumen0.00259470647301078
GO:0048513organ development0.00266446791328663
GO:0031974membrane-enclosed lumen0.00317368745954419
GO:0043233organelle lumen0.00317368745954419
GO:0030326embryonic limb morphogenesis0.00415540629745191
GO:0035113embryonic appendage morphogenesis0.00415540629745191
GO:0048731system development0.00489650441409066
GO:0035107appendage morphogenesis0.00489650441409066
GO:0035108limb morphogenesis0.00489650441409066
GO:0060173limb development0.00489650441409066
GO:0048736appendage development0.00489650441409066
GO:0044428nuclear part0.00551324171480623
GO:0006355regulation of transcription, DNA-dependent0.00551324171480623
GO:0006351transcription, DNA-dependent0.00551324171480623
GO:0032774RNA biosynthetic process0.00551324171480623
GO:0003677DNA binding0.00560995379016853
GO:0045449regulation of transcription0.00578422189955604
GO:0048856anatomical structure development0.00587999880279197
GO:0019219regulation of nucleobase, nucleoside, nucleotide and nucleic acid metabolic process0.00587999880279197
GO:0006350transcription0.00602887185361421
GO:0010468regulation of gene expression0.0067870812496044
GO:0031323regulation of cellular metabolic process0.00790017989892396
GO:0007275multicellular organismal development0.00849566317085947
GO:0019222regulation of metabolic process0.00876372901634206
GO:0016070RNA metabolic process0.00958001881999868
GO:0046332SMAD binding0.0139741292509268
GO:0045843negative regulation of striated muscle development0.0139741292509268
GO:0005518collagen binding0.0139741292509268
GO:0048598embryonic morphogenesis0.0162956286286687
GO:0043234protein complex0.0180532963462087
GO:0010467gene expression0.0183035077001981
GO:0003676nucleic acid binding0.0198566542060702
GO:0035115embryonic forelimb morphogenesis0.0208469733473235
GO:0032502developmental process0.0208469733473235
GO:0016202regulation of striated muscle development0.0208469733473235
GO:0010092specification of organ identity0.0208469733473235
GO:0001759induction of an organ0.0208469733473235
GO:0031128induction0.0215104325091062
GO:0045168cell-cell signaling during cell fate commitment0.0215104325091062
GO:0030246carbohydrate binding0.0216351742869658
GO:0035136forelimb morphogenesis0.022120169814977
GO:0006139nucleobase, nucleoside, nucleotide and nucleic acid metabolic process0.0222185820997572
GO:0005540hyaluronic acid binding0.0226823841787019
GO:0050794regulation of cellular process0.0290204774403076
GO:0032991macromolecular complex0.0299126914371503
GO:0035137hindlimb morphogenesis0.0307801926670324
GO:0050789regulation of biological process0.043652504504262
GO:0044446intracellular organelle part0.0481157019908402
GO:0044422organelle part0.0481157019908402
GO:0009790embryonic development0.0488680045372098



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>

Uber Anatomy
Ontology termp-valuen
forelimb2.69e-177
pectoral appendage2.69e-177
pectoral appendage bud2.69e-177
forelimb bud2.69e-177
forelimb/pectoral fin field2.69e-177
pectoral complex5.66e-158
appendage1.49e-0912
paired limb/fin1.49e-0912
limb1.49e-0912
paired limb/fin bud1.49e-0912
limb bud1.49e-0912
limb/fin field1.49e-0912
limb field1.49e-0912
appendage girdle complex1.01e-0813
surface structure3.05e-0722


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)
MA0003.10.630339
MA0004.10.555731
MA0006.10.228715
MA0007.11.34507
MA0009.10.93858
MA0014.10.181411
MA0017.10.11299
MA0019.10.221321
MA0024.10.322453
MA0025.10.553002
MA0027.11.91746
MA0028.10.099689
MA0029.10.305809
MA0030.10.836147
MA0031.10.284004
MA0038.10.150331
MA0040.10.366712
MA0041.10.397031
MA0042.10.0421363
MA0043.10.435645
MA0046.10.385571
MA0048.10.227772
MA0050.10.311127
MA0051.10.155655
MA0052.10.373177
MA0055.10.263203
MA0056.10
MA0057.13.31814
MA0058.10.64262
MA0059.10.679523
MA0060.11.27911
MA0061.10.310047
MA0063.10
MA0066.10.869432
MA0067.10.652366
MA0068.15.90148
MA0069.10.373449
MA0070.10.365675
MA0071.10.0930503
MA0072.10.358914
MA0073.124.212
MA0074.10.123701
MA0076.10.0318933
MA0077.10.341791
MA0078.10.175945
MA0081.10.192641
MA0083.10.434982
MA0084.10.958921
MA0087.10.399335
MA0088.10.168242
MA0089.10
MA0090.10.0615811
MA0091.10.584863
MA0092.10.833305
MA0093.10.781254
MA0095.10
MA0098.10
MA0100.10.374893
MA0101.10.0468921
MA0103.10.122326
MA0105.10.542683
MA0106.11.02229
MA0107.10.0280799
MA0108.21.24164
MA0109.10
MA0111.10.512045
MA0113.10.163276
MA0114.10.150918
MA0115.10.437985
MA0116.10.435156
MA0117.10.411186
MA0119.10.400754
MA0122.10.427622
MA0124.10.604388
MA0125.10.538769
MA0130.10
MA0131.10.218222
MA0132.10
MA0133.10
MA0135.11.17732
MA0136.10.134737
MA0139.10.027105
MA0140.10.374733
MA0141.10.140263
MA0142.10.27329
MA0143.10.173388
MA0144.10.155067
MA0145.10.831393
MA0146.11.35282
MA0147.10.341028
MA0148.10.0829136
MA0149.10.183385
MA0062.20.00237099
MA0035.20.119926
MA0039.22.74685
MA0138.20.212837
MA0002.20.336369
MA0137.20.322137
MA0104.20.379989
MA0047.20.149878
MA0112.21.61978
MA0065.20.310259
MA0150.10.0692983
MA0151.10
MA0152.11.43731
MA0153.10.480495
MA0154.10.0222139
MA0155.12.5538
MA0156.10.031657
MA0157.10.250083
MA0158.10
MA0159.10.909317
MA0160.10.0842824
MA0161.10
MA0162.11.86634
MA0163.11.23775
MA0164.10.831004
MA0080.20.117725
MA0018.20.140467
MA0099.20.208596
MA0079.217.9282
MA0102.21.0092
MA0258.12.21524
MA0259.10.0586005
MA0442.10
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