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MCL coexpression mm9:162: Difference between revisions

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|ontology_enrichment_disease=
|ontology_enrichment_disease=
|ontology_enrichment_uberon=UBERON:0002107!1.33e-32!22;UBERON:0007499!1.33e-32!22;UBERON:0006925!1.33e-32!22;UBERON:0009497!1.33e-32!22;UBERON:0000015!1.33e-32!22;UBERON:0002423!1.33e-32!22;UBERON:0006235!1.33e-32!22;UBERON:0008835!1.33e-32!22;UBERON:0003894!1.33e-32!22;UBERON:0004161!1.33e-32!22;UBERON:0008836!1.33e-32!22;UBERON:0009854!3.71e-31!23;UBERON:0009856!3.71e-31!23;UBERON:0002365!1.30e-28!25;UBERON:0002330!1.30e-28!25;UBERON:0005256!1.44e-15!45;UBERON:0003914!7.19e-15!47;UBERON:0005172!3.14e-14!49;UBERON:0005173!3.14e-14!49;UBERON:0002417!3.14e-14!49;UBERON:0000916!3.14e-14!49;UBERON:0003929!1.39e-12!55;UBERON:0002368!1.83e-11!60;UBERON:0003104!2.92e-11!61;UBERON:0009142!2.92e-11!61;UBERON:0002530!1.64e-10!65;UBERON:0000490!2.44e-10!66;UBERON:0009569!2.44e-10!66;UBERON:0005911!7.53e-10!69;UBERON:0000949!2.12e-09!72;UBERON:0000466!1.75e-08!79;UBERON:0005177!1.75e-08!79;UBERON:0001041!2.30e-08!80;UBERON:0002100!2.52e-07!90
|ontology_enrichment_uberon=UBERON:0002107!1.33e-32!22;UBERON:0007499!1.33e-32!22;UBERON:0006925!1.33e-32!22;UBERON:0009497!1.33e-32!22;UBERON:0000015!1.33e-32!22;UBERON:0002423!1.33e-32!22;UBERON:0006235!1.33e-32!22;UBERON:0008835!1.33e-32!22;UBERON:0003894!1.33e-32!22;UBERON:0004161!1.33e-32!22;UBERON:0008836!1.33e-32!22;UBERON:0009854!3.71e-31!23;UBERON:0009856!3.71e-31!23;UBERON:0002365!1.30e-28!25;UBERON:0002330!1.30e-28!25;UBERON:0005256!1.44e-15!45;UBERON:0003914!7.19e-15!47;UBERON:0005172!3.14e-14!49;UBERON:0005173!3.14e-14!49;UBERON:0002417!3.14e-14!49;UBERON:0000916!3.14e-14!49;UBERON:0003929!1.39e-12!55;UBERON:0002368!1.83e-11!60;UBERON:0003104!2.92e-11!61;UBERON:0009142!2.92e-11!61;UBERON:0002530!1.64e-10!65;UBERON:0000490!2.44e-10!66;UBERON:0009569!2.44e-10!66;UBERON:0005911!7.53e-10!69;UBERON:0000949!2.12e-09!72;UBERON:0000466!1.75e-08!79;UBERON:0005177!1.75e-08!79;UBERON:0001041!2.30e-08!80;UBERON:0002100!2.52e-07!90
|tfbs_overrepresentation_for_novel_motifs=0.03128,0.000937455,0.0721634,0.27151,0.183219,0.508242,0.108081,0.147931,0.00935984,0.00296501,0.0793816,0.463631,0.0450167,0.0280835,0.726945,0,0.302987,0.810122,0.544594,0.0790777,0.369478,0.0666561,0.0278872,1.10166,0.172466,0.0344857,0.832128,0.339237,0.00930338,0.0726037,0.0575697,0.138901,0.163159,0.068805,0.0220356,0.0010894,0.0341499,0.0972905,0.613351,8.95973e-05,0.436335,0.160718,0.386605,1.90518,0.0516313,0.120832,0.471989,0.371549,1.21561,0.662539,0.282905,0.0415347,0.103707,0.222347,0.233728,0.122329,0.957121,0.228138,0.21871,0.02921,0.803006,0.0441965,1.00793,0.0785999,0.130925,0.316837,0.878384,0.616867,0.39734,0.49015,0.00303626,0.877871,3.06024e-05,0.256208,0.0025184,0.0588386,0.514177,0.451021,0.381241,0.228992,0.887801,0.0980457,0.381206,0.316263,0.182353,2.73636e-07,0.176041,0.0728382,0.0614341,0.763142,0.382871,0.185328,0.447132,0.669745,0.103622,1.36652,0.332808,0.450945,0.0598324,0.00430426,0.146075,0.429522,0.211201,0.0833891,0.282384,0.160216,0.109249,0.363181,0.0026512,0.00236174,0.544025,0.609261,1.77356,0.0825035,0.388387,0.82329,4.61157e-05,0.0492808,0.304507,0.235581,0.720321,1.88074,1.79775,0.782921,0.431518,0.385979,0.816461,0.142099,0.328524,0.327252,0.581258,0.258441,2.28341,0.312955,0.40544,0.00552151,0.86415,1.16029,0.366944,1.11117,0.733971,0.33317,0.149737,0.44397,0.0803297,2.42971,0.477804,1.07297,0.874955,0.10175,0.00954725,1.4487e-06,0.635304,0.0428318,0.311503,0.278572,0.369352,0.390885,0.352838,0.00630371,0.374299,0.181844,0.121963,0.336402,0.572331,0.872987,0.0335404,0.243554,1.3843e-06
}}
}}

Revision as of 17:54, 26 November 2012


Phase1 CAGE Peaks

 Short description
Mm9::chr10:111032948..111032961,+p@chr10:111032948..111032961
+
Mm9::chr10:67599952..67599956,-p@chr10:67599952..67599956
-
Mm9::chr11:116050856..116050864,-p15@Acox1
Mm9::chr11:16642247..16642283,-p@chr11:16642247..16642283
-
Mm9::chr12:16596529..16596541,-p2@Lpin1
Mm9::chr12:33455718..33455731,-p@chr12:33455718..33455731
-
Mm9::chr12:33455776..33455786,-p@chr12:33455776..33455786
-
Mm9::chr12:76700319..76700320,-p@chr12:76700319..76700320
-
Mm9::chr13:24420892..24420904,-p@chr13:24420892..24420904
-
Mm9::chr13:24420993..24421016,-p@chr13:24420993..24421016
-
Mm9::chr13:24422074..24422087,-p@chr13:24422074..24422087
-
Mm9::chr14:41917607..41917623,+p@chr14:41917607..41917623
+
Mm9::chr14:80041947..80041958,-p5@Lect1
Mm9::chr16:23981309..23981342,-p@chr16:23981309..23981342
-
Mm9::chr16:43236088..43236099,+p43@Zbtb20
Mm9::chr18:12801105..12801118,+p@chr18:12801105..12801118
+
Mm9::chr18:13018649..13018664,-p15@Osbpl1a
Mm9::chr18:13018706..13018744,-p10@Osbpl1a
Mm9::chr18:75825791..75825811,-p@chr18:75825791..75825811
-
Mm9::chr19:44079718..44079719,-p@chr19:44079718..44079719
-
Mm9::chr19:5826671..5826746,-p@chr19:5826671..5826746
-
Mm9::chr1:129627925..129627959,+p@chr1:129627925..129627959
+
Mm9::chr1:142278108..142278111,+p@chr1:142278108..142278111
+
Mm9::chr1:152980073..152980094,+p@chr1:152980073..152980094
+
Mm9::chr1:152980097..152980108,+p@chr1:152980097..152980108
+
Mm9::chr1:152980110..152980124,+p@chr1:152980110..152980124
+
Mm9::chr1:152980130..152980141,+p@chr1:152980130..152980141
+
Mm9::chr1:40220289..40220292,-p@chr1:40220289..40220292
-
Mm9::chr1:89470480..89470509,-p3@Ngef
Mm9::chr2:118133412..118133420,-p@chr2:118133412..118133420
-
Mm9::chr2:126378471..126378483,+p4@Slc27a2
Mm9::chr2:126378493..126378504,+p5@Slc27a2
Mm9::chr2:132515856..132515898,+p4@1110034G24Rik
Mm9::chr2:132524238..132524262,-p1@ENSMUST00000147868
Mm9::chr2:169425295..169425296,+p@chr2:169425295..169425296
+
Mm9::chr2:4914307..4914346,-p5@Mcm10
Mm9::chr2:4915515..4915520,+p@chr2:4915515..4915520
+
Mm9::chr2:4922613..4922630,-p4@Mcm10
Mm9::chr2:67808715..67808722,+p@chr2:67808715..67808722
+
Mm9::chr2:67809304..67809319,+p@chr2:67809304..67809319
+
Mm9::chr2:71994483..71994498,-p@chr2:71994483..71994498
-
Mm9::chr2:72011296..72011299,+p@chr2:72011296..72011299
+
Mm9::chr2:72012294..72012308,+p@chr2:72012294..72012308
+
Mm9::chr2:72018109..72018123,+p5@Rapgef4
Mm9::chr3:81799618..81799631,+p@chr3:81799618..81799631
+
Mm9::chr3:86816166..86816175,-p@chr3:86816166..86816175
-
Mm9::chr4:107897933..107897941,-p@chr4:107897933..107897941
-
Mm9::chr4:107897984..107897993,-p@chr4:107897984..107897993
-
Mm9::chr4:150228479..150228494,+p@chr4:150228479..150228494
+
Mm9::chr4:98704584..98704588,+p@chr4:98704584..98704588
+
Mm9::chr5:66475935..66475939,-p@chr5:66475935..66475939
-
Mm9::chr5:87808974..87808979,-p@chr5:87808974..87808979
-
Mm9::chr6:149138217..149138221,+p@chr6:149138217..149138221
+
Mm9::chr7:104106630..104106658,+p@chr7:104106630..104106658
+
Mm9::chr7:15078366..15078390,-p1@ENSMUST00000118150
Mm9::chr7:20277295..20277305,-p@chr7:20277295..20277305
-
Mm9::chr7:56133347..56133350,+p2@ENSMUST00000129551
Mm9::chr8:107628743..107628746,+p@chr8:107628743..107628746
+
Mm9::chr8:116614660..116614666,-p@chr8:116614660..116614666
-
Mm9::chr8:131003594..131003606,+p@chr8:131003594..131003606
+
Mm9::chr8:13201413..13201428,-p@chr8:13201413..13201428
-
Mm9::chr8:25686748..25686755,-p3@Ido2
Mm9::chr8:47922918..47922931,+p@chr8:47922918..47922931
+
Mm9::chr9:106173293..106173301,+p@chr9:106173293..106173301
+
Mm9::chr9:74376459..74376475,-p@chr9:74376459..74376475
-
Mm9::chr9:74713442..74713460,+p@chr9:74713442..74713460
+
Mm9::chr9:74714303..74714318,+p2@Onecut1


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:0006629lipid metabolic process0.0277682095850798
GO:0031529ruffle organization and biogenesis0.0277682095850798
GO:0030948negative regulation of vascular endothelial growth factor receptor signaling pathway0.0277682095850798
GO:0009966regulation of signal transduction0.0277682095850798
GO:0032868response to insulin stimulus0.0277682095850798
GO:0043434response to peptide hormone stimulus0.0277682095850798
GO:0032870cellular response to hormone stimulus0.0277682095850798
GO:0032869cellular response to insulin stimulus0.0277682095850798
GO:0042579microbody0.0277682095850798
GO:0005777peroxisome0.0277682095850798
GO:0031532actin cytoskeleton reorganization0.0371242313547847
GO:0005085guanyl-nucleotide exchange factor activity0.039670377237159
GO:0003997acyl-CoA oxidase activity0.039670377237159
GO:0051056regulation of small GTPase mediated signal transduction0.039670377237159
GO:0044255cellular lipid metabolic process0.0425148821081574
GO:0030947regulation of vascular endothelial growth factor receptor signaling pathway0.0425148821081574
GO:0008195phosphatidate phosphatase activity0.048003657065088



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>

Cell Type
Ontology termp-valuen
metabolising cell2.48e-245
endopolyploid cell2.48e-245
parenchymal cell2.48e-245
polyploid cell2.48e-245
hepatocyte2.48e-245
fibroblast7.41e-091
hepatic stellate cell7.41e-091

Uber Anatomy
Ontology termp-valuen
liver1.33e-3222
epithelial sac1.33e-3222
digestive gland1.33e-3222
epithelium of foregut-midgut junction1.33e-3222
anatomical boundary1.33e-3222
hepatobiliary system1.33e-3222
foregut-midgut junction1.33e-3222
hepatic diverticulum1.33e-3222
liver primordium1.33e-3222
septum transversum1.33e-3222
liver bud1.33e-3222
digestive tract diverticulum3.71e-3123
sac3.71e-3123
exocrine gland1.30e-2825
exocrine system1.30e-2825
trunk mesenchyme1.44e-1545
epithelial tube7.19e-1547
abdomen element3.14e-1449
abdominal segment element3.14e-1449
abdominal segment of trunk3.14e-1449
abdomen3.14e-1449
gut epithelium1.39e-1255
endocrine gland1.83e-1160
mesenchyme2.92e-1161
entire embryonic mesenchyme2.92e-1161
gland1.64e-1065
unilaminar epithelium2.44e-1066
subdivision of trunk2.44e-1066
endo-epithelium7.53e-1069
endocrine system2.12e-0972
immaterial anatomical entity1.75e-0879
trunk region element1.75e-0879
foregut2.30e-0880
trunk2.52e-0790


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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