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Coexpression cluster:C547: Difference between revisions

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|tfbs_overrepresentation_for_novel_motifs=0.443805,0.954273,0.431729,0.241986,0.364884,0.240734,0.812661,2.14258,1.1367,0.574634,0.622824,0.335828,1.32156,0.291158,1.20384,1.29616,0.489874,0.590721,0.983369,1.01095,0.139663,1.97978,0.66224,0.110606,0.170101,0.354732,2.09166,0.658421,0.369737,0.741448,1.10654,0.522822,0.506728,0.593112,1.58626,0.339956,0.0919402,0.241614,0.272549,0.167043,0.0929322,0.556817,1.37821,0.360378,0.789494,0.15988,0.301272,0.603923,1.64163,0.369939,0.960528,1.51255,0.56057,0.592653,0.734926,1.45019,0.118135,0.267557,1.08599,0.266768,0.559896,0.303183,0.423107,1.17513,0.317765,0.4351,0.818746,1.17567,0.513487,1.01727,0.181085,0.442034,0.163729,0.73304,0.569026,0.524857,1.12695,0.450429,1.272,0.165891,0.647118,0.464358,0.317477,0.760881,0.684728,1.84933,0.127301,0.44194,0.38876,1.27332,0.90828,0.659533,0.537982,0.0697368,0.738776,0.947698,0.150074,0.576706,0.392699,0.389681,0.0801198,0.532876,0.571612,0.493139,0.425079,0.214722,0.479058,0.288402,2.22064,0.340143,0.146911,0.569087,0.422755,0.225069,0.862131,1.05534,0.84461,1.10313,1.10556,0.0711462,0.725237,0.386689,1.24731,0.326716,0.968805,0.451097,0.295287,0.542501,0.765493,0.0768182,0.660176,0.5898,0.779127,0.323981,0.920697,0.0195305,0.19775,0.233646,0.879842,1.7239,1.32497,0.844052,0.296675,0.573485,1.09157,0.260955,0.412168,1.56567,1.05096,0.516702,0.766653,0.0731131,0.660531,0.711583,0.302791,1.04704,0.374997,2.30402,0.170141,0.459614,0.842888,1.55192,1.27049,0.464924,0.440625,0.316832,0.486038,0.299321,0.997448
}}
}}

Revision as of 14:18, 26 November 2012


Full id: C547_Renal_Endothelial_Mesenchymal_Hepatic_Smooth_Fibroblast_Alveolar



Phase1 CAGE Peaks

Hg19::chr1:22163333..22163340,-p6@HSPG2
Hg19::chr1:22181125..22181132,-p15@HSPG2
Hg19::chr1:22186101..22186129,-p@chr1:22186101..22186129
-
Hg19::chr1:22203039..22203053,-p@chr1:22203039..22203053
-
Hg19::chr1:22203092..22203119,-p@chr1:22203092..22203119
-
Hg19::chr1:22204962..22204969,-p4@HSPG2
Hg19::chr1:22206973..22206987,-p@chr1:22206973..22206987
-
Hg19::chr1:22207217..22207234,-p@chr1:22207217..22207234
-
Hg19::chr1:22211127..22211133,+p@chr1:22211127..22211133
+
Hg19::chr1:22211913..22211920,+p@chr1:22211913..22211920
+
Hg19::chr1:22213979..22214020,-p@chr1:22213979..22214020
-
Hg19::chr1:22214092..22214113,+p@chr1:22214092..22214113
+
Hg19::chr1:22214103..22214127,-p@chr1:22214103..22214127
-
Hg19::chr1:22214518..22214534,-p@chr1:22214518..22214534
-
Hg19::chr1:22216505..22216565,-p@chr1:22216505..22216565
-
Hg19::chr1:22222766..22222805,-p2@HSPG2
Hg19::chr1:22263793..22263811,-p1@HSPG2


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

No GOStat results

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>

Uber Anatomy
Ontology termp-valuen
splanchnic layer of lateral plate mesoderm2.65e-2783
vessel6.57e-2668
epithelial tube1.96e-24117
epithelial tube open at both ends1.71e-2259
blood vessel1.71e-2259
blood vasculature1.71e-2259
vascular cord1.71e-2259
vasculature7.62e-2278
vascular system7.62e-2278
circulatory system1.22e-19112
cardiovascular system9.41e-19109
artery6.74e-1542
arterial blood vessel6.74e-1542
arterial system6.74e-1542
blood vessel endothelium2.08e-1418
endothelium2.08e-1418
cardiovascular system endothelium2.08e-1418
squamous epithelium3.84e-1425
simple squamous epithelium9.19e-1422
anatomical conduit6.48e-12240
mesoderm9.29e-12315
mesoderm-derived structure9.29e-12315
presumptive mesoderm9.29e-12315
unilaminar epithelium7.04e-11148
systemic artery9.38e-1133
systemic arterial system9.38e-1133
trunk mesenchyme4.84e-10122
mesenchyme3.14e-09160
entire embryonic mesenchyme3.14e-09160
multi-cellular organism4.07e-09656
trunk1.05e-08199
primary circulatory organ1.26e-0827
endothelial tube3.14e-089
arterial system endothelium3.14e-089
endothelium of artery3.14e-089
intermediate mesoderm3.24e-0828
urogenital ridge3.63e-0811
aorta4.25e-0821
aortic system4.25e-0821
epithelial vesicle6.24e-0878
heart8.66e-0824
primitive heart tube8.66e-0824
primary heart field8.66e-0824
anterior lateral plate mesoderm8.66e-0824
heart tube8.66e-0824
heart primordium8.66e-0824
cardiac mesoderm8.66e-0824
cardiogenic plate8.66e-0824
heart rudiment8.66e-0824
compound organ1.59e-0768
organism subdivision1.69e-07264
muscle tissue2.22e-0764
musculature2.22e-0764
musculature of body2.22e-0764
skeletal muscle tissue5.80e-0762
striated muscle tissue5.80e-0762
myotome5.80e-0762
tube6.95e-07192
mesonephros7.15e-079
pronephros7.15e-079
nephrogenic cord7.15e-079
pronephric mesoderm7.15e-079
rostral part of nephrogenic cord7.15e-079
presumptive pronephric mesoderm7.15e-079
epithelium9.60e-07306


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)

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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

No analysis results for this cluster

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

This analysis result is provided for C0 - C305 clusters.

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