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Coexpression cluster:C230: Difference between revisions

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|tf_chipseq_enrich=RAD21#5885;12:2.03705584828649:0.0128043598161993:0.0460700222153181
|tf_chipseq_enrich=RAD21#5885;12:2.03705584828649:0.0128043598161993:0.0460700222153181
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|tfbs_overrepresentation_for_novel_motifs=0.0809908,0.0320858,0.167702,1.04942,0.113035,0.0912613,0.14804,0.020997,0.756107,0.391992,0.0728128,0.186739,0.349478,0.138529,0.36128,0.645125,0.38793,0.356808,0.948116,0.495899,0.72986,0.0195013,0.0862994,0.761994,0.114553,0.458041,0.511811,0.214768,0.803437,0.0419945,0.547251,0.859133,0.257308,0.500274,0.271361,0.110226,0.0737899,0.229701,0.701265,0.132609,0.267853,0.0528835,0.00370797,0.356919,0.225061,0.100632,0.971222,0.871565,0.468711,0.116833,0.484532,0.159064,0.699942,0.185058,0.285549,0.140925,0.387138,0.11539,0.297981,0.114647,0.164079,0.0384029,0.273657,0.109063,0.166587,0.311119,0.350587,0.658583,0.135992,0.516982,0.130295,0.109105,1.69906,0.775783,0.803452,0.113424,0.328023,0.101246,0.134296,0.037813,0.0116815,0.108558,0.673289,1.27577,0.248516,0.038236,5.78904,0.00230114,0.25041,0.748573,0.423767,0.230543,0.897689,1.33029,0.113904,0.0498762,0.178766,0.174731,0.255402,1.79195,0.116991,0.884666,0.171477,0.124329,0.0884977,0.183092,0.116504,0.580323,0.23996,0.320358,0.53239,0.169873,0.476835,0.389105,0.385616,0.823441,1.38664,3.47397,0.638073,0.0936256,0.27828,0.529765,0.224371,0.176466,1.19603,0.681385,0.0358539,0.466104,0.308831,0.320609,1.21831,0.0624214,2.34579,0.173424,0.434176,0.0316946,0.31276,0.215519,0.400154,1.17966,0.796831,0.370915,0.14418,0.51386,0.299676,0.495331,0.0822936,1.02612,0.490801,0.408953,0.0204391,0.899407,0.231247,0.152795,0.347598,0.543107,2.38417,0.0399858,0.0402511,0.193193,0.369974,0.219209,0.41716,0.35541,0.0962285,0.376624,0.362576,0.614907,0.00018331
}}
}}

Revision as of 13:51, 26 November 2012


Full id: C230_aorta_normal_heart_penis_osteosarcoma_basal_lung



Phase1 CAGE Peaks

Hg19::chr10:15646574..15646578,-p11@ITGA8
Hg19::chr10:15760797..15760808,-p@chr10:15760797..15760808
-
Hg19::chr10:15760828..15760842,-p@chr10:15760828..15760842
-
Hg19::chr10:15761845..15761856,-p4@ITGA8
Hg19::chr10:15761884..15761936,-p1@ITGA8
Hg19::chr10:15761954..15761965,-p7@ITGA8
Hg19::chr10:15761966..15761979,-p2@ITGA8
Hg19::chr10:15762207..15762225,-p8@ITGA8
Hg19::chr10:15762227..15762257,-p3@ITGA8
Hg19::chr10:15762274..15762283,-p12@ITGA8
Hg19::chr10:15762312..15762340,-p6@ITGA8
Hg19::chr10:15762346..15762358,-p9@ITGA8
Hg19::chr12:19928351..19928358,+p2@ENST00000535764
Hg19::chr12:19928380..19928401,+p1@ENST00000535764
Hg19::chr13:39952800..39952810,-p@chr13:39952800..39952810
-
Hg19::chr14:92307575..92307589,-p@chr14:92307575..92307589
-
Hg19::chr14:92307596..92307610,-p@chr14:92307596..92307610
-
Hg19::chr14:92307628..92307643,-p@chr14:92307628..92307643
-
Hg19::chr16:2173505..2173521,-p1@AF088750
Hg19::chr16:73127519..73127528,-p@chr16:73127519..73127528
-
Hg19::chr16:73127560..73127571,-p@chr16:73127560..73127571
-
Hg19::chr17:12570155..12570163,+p@chr17:12570155..12570163
+
Hg19::chr1:16084107..16084112,+p19@FBLIM1
Hg19::chr1:163117077..163117096,-p@chr1:163117077..163117096
-
Hg19::chr1:48224242..48224244,+p@chr1:48224242..48224244
+
Hg19::chr22:25466244..25466263,+p8@KIAA1671
Hg19::chr22:25466273..25466284,+p7@KIAA1671
Hg19::chr22:25466305..25466317,+p6@KIAA1671
Hg19::chr2:107467431..107467465,-p@chr2:107467431..107467465
-
Hg19::chr2:18116344..18116353,+p@chr2:18116344..18116353
+
Hg19::chr2:285923..285935,+p1@ENST00000450709
Hg19::chr2:28958958..28958989,-p1@ENST00000444501
Hg19::chr2:28959059..28959099,-p1@ENST00000452212
Hg19::chr2:33285212..33285215,+p@chr2:33285212..33285215
+
Hg19::chr2:33285233..33285259,+p@chr2:33285233..33285259
+
Hg19::chr2:33285264..33285274,+p@chr2:33285264..33285274
+
Hg19::chr3:24231794..24231799,-p38@THRB
Hg19::chr3:29966392..29966406,+p22@RBMS3
Hg19::chr3:33260352..33260365,-p3@SUSD5
Hg19::chr3:33260373..33260422,-p2@SUSD5
Hg19::chr3:33260478..33260490,-p8@SUSD5
Hg19::chr3:33260765..33260770,-p7@SUSD5
Hg19::chr3:57881966..57881977,+p13@SLMAP
Hg19::chr3:57882024..57882045,+p10@SLMAP
Hg19::chr3:57882061..57882085,+p4@SLMAP
Hg19::chr4:106833328..106833353,+p7@NPNT
Hg19::chr4:119860470..119860487,+p@chr4:119860470..119860487
+
Hg19::chr4:15429533..15429568,-p1@ENST00000502344
Hg19::chr4:174846835..174846846,+p@chr4:174846835..174846846
+
Hg19::chr5:122448503..122448506,+p@chr5:122448503..122448506
+
Hg19::chr5:59792105..59792117,-p@chr5:59792105..59792117
-
Hg19::chr6:84743412..84743431,+p2@MRAP2
Hg19::chr6:84743436..84743496,+p1@MRAP2
Hg19::chr7:40549076..40549087,+p@chr7:40549076..40549087
+
Hg19::chr7:40549088..40549102,+p@chr7:40549088..40549102
+
Hg19::chr7:73462921..73462932,+p@chr7:73462921..73462932
+
Hg19::chr7:73468280..73468302,-p@chr7:73468280..73468302
-
Hg19::chr8:120428678..120428695,+p1@NOV
Hg19::chr8:120430391..120430409,+p@chr8:120430391..120430409
+
Hg19::chr8:120435183..120435195,-p1@CU677182
Hg19::chr8:97398865..97398877,-p1@ENST00000523862


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

No results for this coexpression

Enriched Gene Ontology terms on this co-expression cluster<b>Summary:</b> Results for GOStat analysis on co-expressed clusters. Each cluster with promoters mapping to at least two different genes was analysed with GOStat (PMID: 14962934) with default parameter. <br><b>Analyst:</b> Erik Arner<br><br>link to source dataset<br>data

GO IDGO nameFDR corrected p-value
GO:0022610biological adhesion0.00609452779185376
GO:0007155cell adhesion0.00609452779185376
GO:0000902cell morphogenesis0.00933294408204043
GO:0032989cellular structure morphogenesis0.00933294408204043
GO:0030511positive regulation of transforming growth factor beta receptor signaling pathway0.0436562672371586
GO:0032501multicellular organismal process0.0436562672371586
GO:0005515protein binding0.0455961126751561
GO:0009653anatomical structure morphogenesis0.0455961126751561
GO:0004887thyroid hormone receptor activity0.0493564118487119
GO:0007613memory0.0493564118487119
GO:0005790smooth endoplasmic reticulum0.0493564118487119



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
adult organism3.12e-37114
meninx2.02e-122
membrane organ2.02e-122
meningeal cluster2.02e-122
valve9.70e-093
cardiac mesenchyme9.70e-093
cardial valve9.70e-093
tunica intima9.70e-093
heart layer9.70e-093
endocardium9.70e-093
endocardial cushion9.70e-093
presumptive endocardium9.70e-093
pulmonary valve3.13e-071
semi-lunar valve3.13e-071
penis3.32e-071
intromittent organ3.32e-071
lateral plate mesenchyme3.32e-071
undifferentiated genital tubercle3.32e-071
somatopleure3.32e-071
mitral valve3.95e-071
dura mater4.18e-071
future meninx4.18e-071
ectomeninx4.18e-071
future dura mater4.18e-071
uterus or analog4.69e-071
epididymis6.99e-071


Overrepresented TFBS (DNA) motifs on this co-expression cluster<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}}}



ENCODE TF ChIP-seq peak enrichment analysis<b>Summary:</b> For each TF and each co-expression cluster, the number of promoters with ENCODE TF ChIP signal was compared with the rest of promoters from the robust set using Fisher's exact test. Clusters with significant ChIP enrichment (q <= 0.05) after Benjamini-Hochberg correction were retained. <br><b>Analyst:</b> Erik Arner<br><br>link to source dataset<br><br>data

(#promoters = Number of promoters in this coexpression cluster that have ChIP signal of the TF)

TF#promotersEnrichmentp-valueq-value
RAD21#5885122.037055848286490.01280435981619930.0460700222153181



Relative expression of the co-expression cluster<b>Summary:</b>Co-expression clusters are compared against FANTOM5 samples to obtain relative expression. <br><b>Analyst:</b>NA<br><br>link to data source<br> data

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