Personal tools

MCL coexpression mm9:1244: Difference between revisions

From FANTOM5_SSTAR

Jump to: navigation, search
(Created page with "{{MCL_coexpression_mm9|gostat_on_MCL_coexpression=GO:0043565;sequence-specific DNA binding;0.00128041237870629;15395,13982,15396!GO:0003700;transcription factor activity;0.004...")
 
No edit summary
Line 1: Line 1:
{{MCL_coexpression_mm9|gostat_on_MCL_coexpression=GO:0043565;sequence-specific DNA binding;0.00128041237870629;15395,13982,15396!GO:0003700;transcription factor activity;0.00425779343150948;15395,13982,15396!GO:0009653;anatomical structure morphogenesis;0.00745703692690638;15395,13982,15396!GO:0045839;negative regulation of mitosis;0.00821737696392652;13982!GO:0007389;pattern specification process;0.00916575112443743;15395,15396!GO:0006355;regulation of transcription, DNA-dependent;0.00916575112443743;15395,13982,15396!GO:0006351;transcription, DNA-dependent;0.00916575112443743;15395,13982,15396!GO:0032774;RNA biosynthetic process;0.00916575112443743;15395,13982,15396!GO:0003677;DNA binding;0.00916575112443743;15395,13982,15396!GO:0045449;regulation of transcription;0.00916575112443743;15395,13982,15396!GO:0048856;anatomical structure development;0.00916575112443743;15395,13982,15396!GO:0019219;regulation of nucleobase, nucleoside, nucleotide and nucleic acid metabolic process;0.00916575112443743;15395,13982,15396!GO:0006350;transcription;0.00916575112443743;15395,13982,15396!GO:0010468;regulation of gene expression;0.0093978923010452;15395,13982,15396!GO:0031323;regulation of cellular metabolic process;0.00961506158071779;15395,13982,15396!GO:0005667;transcription factor complex;0.00961506158071779;15395,15396!GO:0019222;regulation of metabolic process;0.0097359320341928;15395,13982,15396!GO:0016070;RNA metabolic process;0.00994272197671441;15395,13982,15396!GO:0001759;induction of an organ;0.00997226994819038;15396!GO:0010092;specification of organ identity;0.00997226994819038;15396!GO:0009887;organ morphogenesis;0.00997226994819038;15395,15396!GO:0045168;cell-cell signaling during cell fate commitment;0.00997226994819038;15396!GO:0031128;induction;0.00997226994819038;15396!GO:0044451;nucleoplasm part;0.00997226994819038;15395,15396!GO:0005654;nucleoplasm;0.0105053104482289;15395,15396!GO:0010467;gene expression;0.0117982004492543;15395,13982,15396!GO:0003676;nucleic acid binding;0.0122037722687037;15395,13982,15396!GO:0032502;developmental process;0.0127500285248328;15395,13982,15396!GO:0031981;nuclear lumen;0.0127500285248328;15395,15396!GO:0006139;nucleobase, nucleoside, nucleotide and nucleic acid metabolic process;0.0137472389941103;15395,13982,15396!GO:0007088;regulation of mitosis;0.0142119381120271;13982!GO:0031974;membrane-enclosed lumen;0.0142119381120271;15395,15396!GO:0043233;organelle lumen;0.0142119381120271;15395,15396!GO:0050794;regulation of cellular process;0.0149611027976701;15395,13982,15396!GO:0050789;regulation of biological process;0.0200777394008583;15395,13982,15396!GO:0001656;metanephros development;0.0201764519006285;15396!GO:0005496;steroid binding;0.0201764519006285;13982!GO:0003707;steroid hormone receptor activity;0.0201764519006285;13982!GO:0004879;ligand-dependent nuclear receptor activity;0.0201764519006285;13982!GO:0044428;nuclear part;0.0205358236401176;15395,15396!GO:0065007;biological regulation;0.0229268067524417;15395,13982,15396!GO:0005634;nucleus;0.0238045419967062;15395,13982,15396!GO:0043283;biopolymer metabolic process;0.025483047988348;15395,13982,15396!GO:0001822;kidney development;0.027160817266496;15396!GO:0001655;urogenital system development;0.0287305713925266;15396!GO:0048513;organ development;0.0325860332208126;15395,15396!GO:0016049;cell growth;0.0327041000229519;13982!GO:0045165;cell fate commitment;0.0340555540588183;15396!GO:0008361;regulation of cell size;0.0352516481138001;13982!GO:0005515;protein binding;0.0352516481138001;15395,13982,15396!GO:0045786;negative regulation of progression through cell cycle;0.0371480088490407;13982!GO:0043234;protein complex;0.03962013826808;15395,15396!GO:0048731;system development;0.0425824276148522;15395,15396!GO:0003002;regionalization;0.0443845586634856;15396!GO:0043170;macromolecule metabolic process;0.0451761693242856;15395,13982,15396!GO:0007067;mitosis;0.0482831052960478;13982!GO:0000087;M phase of mitotic cell cycle;0.0482831052960478;13982!GO:0000074;regulation of progression through cell cycle;0.0496525167121281;13982!GO:0001501;skeletal development;0.0496525167121281;15396!}}
{{MCL_coexpression_mm9
|coexpression_dpi_cluster_scores_mean=0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0.468810951402817,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0.0111309898120793,0,0,0,0,0,0,0,0.0457421522525172,0,0.0317518424311083,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0.139092637649875,0.244595961508259,0.165248047545539,0,0,0,0,0,0.356679314741001,0.307616679637004,0,0,0,0,0.00869811735157467,0,0,0,0,0,0,0.0102922179483632,0.39853536447891,0.491946602877576,0.42584706310329,0,0.0105464367459272,0,0,0,0,0,0,0.110599436096358,0.188528732259936,0.122284614798021,0.146513963861889,0,0.0920409710752248,0,0,0,0,0,0.118808011695809,0,0,0.0878790634259986,0.0192387650524658,0.131630261678882,0,0.0466704488455586,0.00856829614165247,0.428374285964944,0.026081331947918,0,0.195492896508995,0.097060350309906,0.154094460964877,0.228480260119283,0,0,0,0,0,0,0.018967241077451,0,0,0,0.0164818733780083,0,0,0.737178910723469,0.234397092294514,0.016309161233149,0,0,0,0,0,0,0,0,0,1.09785023116919,0.855119442611945,0.866420878789601,0.727652941305435,0.728812882671012,0.508247053220969,0.540707114826968,0.292791171211265,0,0,0,0.0136254203921497,0.0152500436695449,0,0,0,0,0,0,0,0,0,0,0,0.0143666085988154,0,0,0,0,0.033967285130882,0.400189449448965,0.3187214237052,0.220553408278104,0.145704592617229,0.142102772886998,0.209036012991248,0,0.10579402103805,0.265261501055835,0.260041296466471,0.236450810429648,0,0.249902786279707,0.260035414670979,0.954560978491945,0.780285520047849,0.810456153520813,0.765518798541372,0.74373438210103,0.685023132192468,0.708052751081334,0.342357888020756,0.380375234615931,0.341672957885554,0,0,0.0129890193201731,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0.0125602184568965,0.0109277726371718,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0.104974676366518,0,0,0,0,0,0,0,0,0,0,0.484339908017807,0.918157830659299,0.978636538134867,1.38512467893755,0,0,0,0,0.0187285000299395,0.0346896076909302,0,0,0,0,0,0,0.0719528621386508,0.0582152336478528,0,0,0,0,0.0110262957459347,0,1.60175381536208,0.875616757131044,0.444332355237358,0.0290903419121132,0.146060423245323,0.116118545397538,0.124818800630638,0.111457224789475,0,0.0922387155006588,0,0.0135811001783894,0,0,0.009273942432869,0,0.0113629758435916,0,0,0,0.10232706763359,0.161326104373072,0,0,0,0.00915732535949133,0,0,0.362806839347608,0,0,0.0100858711413906,0.0332484050430722,0.0257228022853725,0.0477321896759112,0.0112997018439347,0.12549549150626,0.298619738121252,0.0144356643696644,0,0,0,0.0133610693509637,0,0,0,0,0,0,0,0,0,0.00673131024600907,0,0,0,0,0.0172516782248752,0.0112333229753319,0.696667936582203,1.58692967303083,1.26958775587664,0.724371940448675,0.41208407202185,0,0,0,0,0,0,0,0,0,0,0.441369263484612,0.319028615991865,0.3169710988747,0.241416589846291,0.277700078054385,0.190574281876271,0.160610709512668,0.120446083158575,0.109249240335887,0.160208422740209,0.147383618249096,0.088876504789783,0.190549589696283,0.203573636596675,0.1838871158731,0.250696077142614,0.168130794925726,0.177664492583089,0.266543668146463,0.172858900395307,0.140024998598594,0.173512987665772,0.199302544705124,0.206736602805934,0.230431039063871,0.171410279467435,0.134144686192592,0.176831880222325,0.191444743645688,0.168187600283249,0.205529452154477,0.143956189592825,0.209249532809908,0.153868910714321,0.227917069276798,0,0.20896427015246,0.227931157606161,0.255723986815329,0.197970583803891,0.202799952191475
|gostat_on_MCL_coexpression=GO:0043565;sequence-specific DNA binding;0.00128041237870629;15395,13982,15396!GO:0003700;transcription factor activity;0.00425779343150948;15395,13982,15396!GO:0009653;anatomical structure morphogenesis;0.00745703692690638;15395,13982,15396!GO:0045839;negative regulation of mitosis;0.00821737696392652;13982!GO:0007389;pattern specification process;0.00916575112443743;15395,15396!GO:0006355;regulation of transcription, DNA-dependent;0.00916575112443743;15395,13982,15396!GO:0006351;transcription, DNA-dependent;0.00916575112443743;15395,13982,15396!GO:0032774;RNA biosynthetic process;0.00916575112443743;15395,13982,15396!GO:0003677;DNA binding;0.00916575112443743;15395,13982,15396!GO:0045449;regulation of transcription;0.00916575112443743;15395,13982,15396!GO:0048856;anatomical structure development;0.00916575112443743;15395,13982,15396!GO:0019219;regulation of nucleobase, nucleoside, nucleotide and nucleic acid metabolic process;0.00916575112443743;15395,13982,15396!GO:0006350;transcription;0.00916575112443743;15395,13982,15396!GO:0010468;regulation of gene expression;0.0093978923010452;15395,13982,15396!GO:0031323;regulation of cellular metabolic process;0.00961506158071779;15395,13982,15396!GO:0005667;transcription factor complex;0.00961506158071779;15395,15396!GO:0019222;regulation of metabolic process;0.0097359320341928;15395,13982,15396!GO:0016070;RNA metabolic process;0.00994272197671441;15395,13982,15396!GO:0001759;induction of an organ;0.00997226994819038;15396!GO:0010092;specification of organ identity;0.00997226994819038;15396!GO:0009887;organ morphogenesis;0.00997226994819038;15395,15396!GO:0045168;cell-cell signaling during cell fate commitment;0.00997226994819038;15396!GO:0031128;induction;0.00997226994819038;15396!GO:0044451;nucleoplasm part;0.00997226994819038;15395,15396!GO:0005654;nucleoplasm;0.0105053104482289;15395,15396!GO:0010467;gene expression;0.0117982004492543;15395,13982,15396!GO:0003676;nucleic acid binding;0.0122037722687037;15395,13982,15396!GO:0032502;developmental process;0.0127500285248328;15395,13982,15396!GO:0031981;nuclear lumen;0.0127500285248328;15395,15396!GO:0006139;nucleobase, nucleoside, nucleotide and nucleic acid metabolic process;0.0137472389941103;15395,13982,15396!GO:0007088;regulation of mitosis;0.0142119381120271;13982!GO:0031974;membrane-enclosed lumen;0.0142119381120271;15395,15396!GO:0043233;organelle lumen;0.0142119381120271;15395,15396!GO:0050794;regulation of cellular process;0.0149611027976701;15395,13982,15396!GO:0050789;regulation of biological process;0.0200777394008583;15395,13982,15396!GO:0001656;metanephros development;0.0201764519006285;15396!GO:0005496;steroid binding;0.0201764519006285;13982!GO:0003707;steroid hormone receptor activity;0.0201764519006285;13982!GO:0004879;ligand-dependent nuclear receptor activity;0.0201764519006285;13982!GO:0044428;nuclear part;0.0205358236401176;15395,15396!GO:0065007;biological regulation;0.0229268067524417;15395,13982,15396!GO:0005634;nucleus;0.0238045419967062;15395,13982,15396!GO:0043283;biopolymer metabolic process;0.025483047988348;15395,13982,15396!GO:0001822;kidney development;0.027160817266496;15396!GO:0001655;urogenital system development;0.0287305713925266;15396!GO:0048513;organ development;0.0325860332208126;15395,15396!GO:0016049;cell growth;0.0327041000229519;13982!GO:0045165;cell fate commitment;0.0340555540588183;15396!GO:0008361;regulation of cell size;0.0352516481138001;13982!GO:0005515;protein binding;0.0352516481138001;15395,13982,15396!GO:0045786;negative regulation of progression through cell cycle;0.0371480088490407;13982!GO:0043234;protein complex;0.03962013826808;15395,15396!GO:0048731;system development;0.0425824276148522;15395,15396!GO:0003002;regionalization;0.0443845586634856;15396!GO:0043170;macromolecule metabolic process;0.0451761693242856;15395,13982,15396!GO:0007067;mitosis;0.0482831052960478;13982!GO:0000087;M phase of mitotic cell cycle;0.0482831052960478;13982!GO:0000074;regulation of progression through cell cycle;0.0496525167121281;13982!GO:0001501;skeletal development;0.0496525167121281;15396!
}}

Revision as of 11:21, 11 October 2012


Phase1 CAGE Peaks

 Short description
Mm9::chr10:5636678..5636725,-p6@Esr1
Mm9::chr6:52190656..52190667,-p7@Hoxa10
Mm9::chr6:52190668..52190682,-p3@Hoxa10
Mm9::chr6:52195747..52195762,-p3@Hoxa11
Mm9::chr6:52195763..52195792,-p2@Hoxa11
Mm9::chr6:52195795..52195825,-p1@Hoxa11


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 binding0.00128041237870629
GO:0003700transcription factor activity0.00425779343150948
GO:0009653anatomical structure morphogenesis0.00745703692690638
GO:0045839negative regulation of mitosis0.00821737696392652
GO:0007389pattern specification process0.00916575112443743
GO:0006355regulation of transcription, DNA-dependent0.00916575112443743
GO:0006351transcription, DNA-dependent0.00916575112443743
GO:0032774RNA biosynthetic process0.00916575112443743
GO:0003677DNA binding0.00916575112443743
GO:0045449regulation of transcription0.00916575112443743
GO:0048856anatomical structure development0.00916575112443743
GO:0019219regulation of nucleobase, nucleoside, nucleotide and nucleic acid metabolic process0.00916575112443743
GO:0006350transcription0.00916575112443743
GO:0010468regulation of gene expression0.0093978923010452
GO:0031323regulation of cellular metabolic process0.00961506158071779
GO:0005667transcription factor complex0.00961506158071779
GO:0019222regulation of metabolic process0.0097359320341928
GO:0016070RNA metabolic process0.00994272197671441
GO:0001759induction of an organ0.00997226994819038
GO:0010092specification of organ identity0.00997226994819038
GO:0009887organ morphogenesis0.00997226994819038
GO:0045168cell-cell signaling during cell fate commitment0.00997226994819038
GO:0031128induction0.00997226994819038
GO:0044451nucleoplasm part0.00997226994819038
GO:0005654nucleoplasm0.0105053104482289
GO:0010467gene expression0.0117982004492543
GO:0003676nucleic acid binding0.0122037722687037
GO:0032502developmental process0.0127500285248328
GO:0031981nuclear lumen0.0127500285248328
GO:0006139nucleobase, nucleoside, nucleotide and nucleic acid metabolic process0.0137472389941103
GO:0007088regulation of mitosis0.0142119381120271
GO:0031974membrane-enclosed lumen0.0142119381120271
GO:0043233organelle lumen0.0142119381120271
GO:0050794regulation of cellular process0.0149611027976701
GO:0050789regulation of biological process0.0200777394008583
GO:0001656metanephros development0.0201764519006285
GO:0005496steroid binding0.0201764519006285
GO:0003707steroid hormone receptor activity0.0201764519006285
GO:0004879ligand-dependent nuclear receptor activity0.0201764519006285
GO:0044428nuclear part0.0205358236401176
GO:0065007biological regulation0.0229268067524417
GO:0005634nucleus0.0238045419967062
GO:0043283biopolymer metabolic process0.025483047988348
GO:0001822kidney development0.027160817266496
GO:0001655urogenital system development0.0287305713925266
GO:0048513organ development0.0325860332208126
GO:0016049cell growth0.0327041000229519
GO:0045165cell fate commitment0.0340555540588183
GO:0008361regulation of cell size0.0352516481138001
GO:0005515protein binding0.0352516481138001
GO:0045786negative regulation of progression through cell cycle0.0371480088490407
GO:0043234protein complex0.03962013826808
GO:0048731system development0.0425824276148522
GO:0003002regionalization0.0443845586634856
GO:0043170macromolecule metabolic process0.0451761693242856
GO:0007067mitosis0.0482831052960478
GO:0000087M phase of mitotic cell cycle0.0482831052960478
GO:0000074regulation of progression through cell cycle0.0496525167121281
GO:0001501skeletal development0.0496525167121281



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



"{{{coexpression_dpi_cluster_scores_median}}}" is not a number.

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}}}