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Difference between revisions of "Coexpression cluster:C538"

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|tf_chipseq_enrich=SMARCB1#6598;6:6.44213498158497:0.000197513604963961:0.00237323094671319!ZNF263#10127;6:2.90182646012142:0.0121295164888246:0.043984395422949
 
|tf_chipseq_enrich=SMARCB1#6598;6:6.44213498158497:0.000197513604963961:0.00237323094671319!ZNF263#10127;6:2.90182646012142:0.0121295164888246:0.043984395422949
 
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 +
|tfbs_overrepresentation_for_novel_motifs=1.40379,0.142307,0.139625,0.678862,0.11364,0.675949,0.300393,0.0518257,0.0507535,0.118722,0.218065,0.335828,0.0341672,0.291158,0.733068,0.3998,0.489874,0.590721,0.0386732,0.0465461,0.851351,1.97978,0.234854,0.722974,0.170101,0.354732,0.275679,0.233219,0.115495,0.0226422,0.202067,0.522822,0.0662338,0.326663,0.0937035,0.128004,0.0919402,0.241614,0.574398,0.04349,0.309718,0.556817,0.0266027,0.111922,0.00338453,0.936595,0.814646,0.21008,0.0226973,0.745498,0.366671,0.310813,0.167715,0.592653,0.734926,0.293507,0.118135,0.267557,0.0226107,0.266768,0.559896,0.303183,0.742828,0.465305,0.317765,0.4351,0.818746,1.17567,0.513487,1.01727,0.181085,0.200127,0.326704,0.73304,0.0326098,0.118275,0.0244505,0.450429,0.510572,0.165891,0.0404655,0.464358,2.33641,0.0530449,0.684728,0.341004,0.263183,0.0933568,0.38876,1.27332,0.90828,0.659533,2.28604,0.245209,3.83892,0.0763304,0.150074,0.576706,0.392699,0.0784744,0.0801198,0.532876,0.571612,0.493139,1.08826,0.214722,0.479058,1.43166,0.507144,0.104263,0.146911,0.569087,0.83595,0.225069,0.862131,0.091073,0.0757057,0.201199,0.433061,0.0711462,0.725237,0.386689,1.24731,0.326716,0.968805,0.451097,0.295287,0.542501,0.765493,0.561324,0.660176,0.204142,0.779127,0.323981,0.920697,0.0195305,0.574529,0.233646,0.879842,1.7239,1.32497,1.96733,0.296675,0.573485,0.426604,0.260955,0.412168,1.56567,0.188015,0.0681329,0.0532623,0.717027,0.660531,0.047435,0.302791,1.04704,0.978867,0.105422,0.170141,0.150717,0.842888,0.643319,0.509866,0.152845,0.440625,0.316832,0.0623453,0.810238,0.341372
 
}}
 
}}

Revision as of 05:17, 26 November 2012


Full id: C538_left_skeletal_heart_seminal_ductus_adipose_mature



Phase1 CAGE Peaks

  Short description
Hg19::chr12:10856713..10856723,- p23@CSDA
Hg19::chr17:58042483..58042495,+ p2@ENST00000501190
p2@uc002iye.1
Hg19::chr5:79026919..79026926,+ p@chr5:79026919..79026926
+
Hg19::chr5:79029312..79029328,+ p9@CMYA5
Hg19::chr7:95214018..95214046,- p@chr7:95214018..95214046
-
Hg19::chr7:95218981..95219000,- p12@PDK4
Hg19::chr7:95222151..95222232,- p7@PDK4
Hg19::chr7:95223041..95223065,- p@chr7:95223041..95223065
-
Hg19::chr7:95224363..95224402,- p@chr7:95224363..95224402
-
Hg19::chr7:95224413..95224447,- p@chr7:95224413..95224447
-
Hg19::chr7:95224469..95224481,- p@chr7:95224469..95224481
-
Hg19::chr7:95225490..95225542,- p3@PDK4
Hg19::chr7:95225580..95225618,- p4@PDK4
Hg19::chr7:95225631..95225666,- p2@PDK4
Hg19::chr7:95225695..95225721,- p8@PDK4
Hg19::chr7:95225729..95225740,- p6@PDK4
Hg19::chr7:95225768..95225967,- p1@PDK4


Enriched pathways on this co-expression clusterSummary:
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.
Analyst: Emmanuel Dimont

link to source dataset
data


No results for this coexpression

Enriched Gene Ontology terms on this co-expression clusterSummary: 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.
Analyst: Erik Arner

link to source dataset
data


GO IDGO nameFDR corrected p-value
GO:0004740pyruvate dehydrogenase (acetyl-transferring) kinase activity0.0252486593058398
GO:0009409response to cold0.0252486593058398
GO:0018106peptidyl-histidine phosphorylation0.0252486593058398
GO:0018202peptidyl-histidine modification0.0252486593058398
GO:0004673protein histidine kinase activity0.0419458539477759
GO:0009266response to temperature stimulus0.0419458539477759
GO:0016775phosphotransferase activity, nitrogenous group as acceptor0.0419458539477759



Enriched sample ontology terms on this co-expression clusterSummary: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. Analyst: Hideya Kawaji

links to source dataset

cell_data
uberon_data


Cell Type
Ontology termp-valuen
fat cell5.61e-0915
Uber Anatomy
Ontology termp-valuen
adult organism2.35e-67114
neural tube1.57e-1656
neural rod1.57e-1656
future spinal cord1.57e-1656
neural keel1.57e-1656
regional part of nervous system8.31e-1553
regional part of brain8.31e-1553
neural plate5.42e-1382
presumptive neural plate5.42e-1382
neurectoderm5.38e-1286
central nervous system1.11e-1181
neural nucleus6.98e-119
nucleus of brain6.98e-119
brain9.26e-1168
future brain9.26e-1168
organ system subdivision1.26e-10223
brain grey matter1.95e-1034
gray matter1.95e-1034
regional part of forebrain1.98e-1041
forebrain1.98e-1041
anterior neural tube1.98e-1041
future forebrain1.98e-1041
structure with developmental contribution from neural crest2.18e-10132
ecto-epithelium3.54e-10104
brainstem6.94e-106
nervous system9.46e-1089
telencephalon4.26e-0934
regional part of telencephalon1.15e-0832
basal ganglion2.53e-089
nuclear complex of neuraxis2.53e-089
aggregate regional part of brain2.53e-089
collection of basal ganglia2.53e-089
cerebral subcortex2.53e-089
telencephalic nucleus2.54e-087
anatomical cluster4.64e-08373
posterior neural tube8.50e-0815
chordal neural plate8.50e-0815
organ1.42e-07503
multi-tissue structure1.84e-07342
cerebral hemisphere2.17e-0732
male genital duct3.54e-073
internal male genitalia3.54e-073
anatomical conduit4.74e-07240
corpus striatum6.22e-074
striatum6.22e-074
ventral part of telencephalon6.22e-074
future corpus striatum6.22e-074
valve7.28e-073
cardiac mesenchyme7.28e-073
cardial valve7.28e-073
tunica intima7.28e-073
heart layer7.28e-073
endocardium7.28e-073
endocardial cushion7.28e-073
presumptive endocardium7.28e-073


Overrepresented TFBS (DNA) motifs on this co-expression clusterSummary: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. Analyst: Michiel de Hoon

link to source data
Novel motifs
data

Jaspar motifs
data


Novel motifs



JASPAR motifs

Motifs-log10(p-value)

{{{tfbs_overrepresentation_jaspar}}}



ENCODE TF ChIP-seq peak enrichment analysisSummary: 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.
Analyst: Erik Arner

link to source dataset

data


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

TF#promotersEnrichmentp-valueq-value
SMARCB1#659866.442134981584970.0001975136049639610.00237323094671319
ZNF263#1012762.901826460121420.01212951648882460.043984395422949



Relative expression of the co-expression clusterSummary:Co-expression clusters are compared against FANTOM5 samples to obtain relative expression.
Analyst:NA

link to data source
data


This analysis result is provided for C0 - C305 clusters.