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Coexpression cluster:C4437: Difference between revisions

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|tf_chipseq_enrich=BCL11A#53335;3:28.3694551036071:4.37778126761649e-05:0.000779425669636206!CEBPB#1051;3:7.97114762582482:0.00197418705528856:0.0115605338865871!EP300#2033;3:6.7739417262232:0.00321688050010379:0.0168101562368828!FOS#2353;3:8.9979553088944:0.00137249927241713:0.00900618569439385!GATA2#2624;3:12.744931733554:0.000482952770428379:0.00438372191819655!HDAC2#3066;3:13.4156202366263:0.000414076139985721:0.00392821309691786!JUN#3725;3:12.5128291923363:0.000510331399272625:0.00445714174683339!JUND#3727;3:6.99466394187103:0.00292184504273499:0.0157369178700531!POU5F1#5460;3:335.439201451906:2.63510205045339e-08:1.82377351257324e-06!RAD21#5885;3:10.3550338954563:0.000900491207356542:0.00667090375976095!SP1#6667;3:5.6983813781409:0.00540396270171217:0.0247537044124613!TCF7L2#6934;3:10.7701765631373:0.000800318129839838:0.00616313413673078!TRIM28#10155;3:18.5905250452625:0.000155596929725528:0.00197693281552365
|tf_chipseq_enrich=BCL11A#53335;3:28.3694551036071:4.37778126761649e-05:0.000779425669636206!CEBPB#1051;3:7.97114762582482:0.00197418705528856:0.0115605338865871!EP300#2033;3:6.7739417262232:0.00321688050010379:0.0168101562368828!FOS#2353;3:8.9979553088944:0.00137249927241713:0.00900618569439385!GATA2#2624;3:12.744931733554:0.000482952770428379:0.00438372191819655!HDAC2#3066;3:13.4156202366263:0.000414076139985721:0.00392821309691786!JUN#3725;3:12.5128291923363:0.000510331399272625:0.00445714174683339!JUND#3727;3:6.99466394187103:0.00292184504273499:0.0157369178700531!POU5F1#5460;3:335.439201451906:2.63510205045339e-08:1.82377351257324e-06!RAD21#5885;3:10.3550338954563:0.000900491207356542:0.00667090375976095!SP1#6667;3:5.6983813781409:0.00540396270171217:0.0247537044124613!TCF7L2#6934;3:10.7701765631373:0.000800318129839838:0.00616313413673078!TRIM28#10155;3:18.5905250452625:0.000155596929725528:0.00197693281552365
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|tfbs_overrepresentation_for_novel_motifs=0.699513,0.14394,0.690871,0.855819,1.54806,0.853988,0.937929,0.494933,0.491742,0.221898,0.820209,0.985163,0.436625,0.925331,1.54465,1.60265,1.17594,0.575162,0.452865,0.305559,1.65118,0.242883,0.845342,0.635379,0.743951,1.00973,1.05396,0.842925,0.645155,1.00813,0.795576,1.21459,2.27558,0.439574,0.599922,0.137917,0.596053,0.855276,1.39264,0.469078,0.598234,0.777097,0.259059,0.63803,0.151453,0.726632,0.939121,0.808003,0.247669,0.645308,1.02504,0.951993,0.336258,1.29475,1.45259,0.928548,0.650353,0.892517,0.388177,0.891404,1.25741,0.941709,0.492369,1.14672,0.961293,1.11026,1.54311,1.91674,1.2037,1.75271,0.762094,0.502203,0.333216,1.45054,0.430728,0.414196,1.81344,1.12884,1.20029,5.62051,0.459024,1.14559,0.960908,0.498519,1.39759,0.169933,0.303648,0.381882,1.053,2.0169,1.63834,1.36973,1.23218,1.34254,0.642354,0.560075,1.14422,1.27663,1.05794,0.360456,0.569121,1.22626,1.27082,1.1798,1.09802,0.815119,1.16312,0.921547,0.743661,0.622396,2.82056,1.26794,0.684398,0.830777,1.58942,0.594137,0.188952,0.794219,1.10778,0.547323,1.44203,1.0504,1.98143,0.973172,1.70203,1.12965,0.930979,1.2374,1.48578,0.561252,1.37044,0.798812,1.50051,0.969553,1.65144,0.372828,0.788803,0.843556,1.60823,2.47382,2.06967,1.57016,0.932872,1.27296,1.09989,0.883164,1.08214,2.31409,0.773313,0.539692,0.318511,0.250511,3.03644,2.09999,0.941179,1.78371,1.03563,0.624795,0.744018,0.710709,1.56892,1.35169,1.19946,1.69998,1.11698,0.960047,0.524529,2.15653,0.0768232
}}
}}

Revision as of 16:44, 26 November 2012


Full id: C4437_astrocytoma_Endothelial_testicular_mesothelioma_Renal_teratocarcinoma_iPS



Phase1 CAGE Peaks

Hg19::chr4:85791617..85791626,-p@chr4:85791617..85791626
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Hg19::chr4:85791647..85791659,-p@chr4:85791647..85791659
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Hg19::chr4:85791667..85791699,-p@chr4:85791667..85791699
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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
blood vessel endothelium6.56e-4718
endothelium6.56e-4718
cardiovascular system endothelium6.56e-4718
simple squamous epithelium7.15e-4322
squamous epithelium3.11e-3725
endothelial tube8.48e-359
arterial system endothelium8.48e-359
endothelium of artery8.48e-359
vessel2.71e-2068
vasculature5.21e-1778
vascular system5.21e-1778
epithelial tube open at both ends2.15e-1359
blood vessel2.15e-1359
blood vasculature2.15e-1359
vascular cord2.15e-1359
cardiovascular system6.58e-12109
lymphatic vessel7.03e-128
lymph vasculature7.03e-128
lymphatic part of lymphoid system7.03e-128
circulatory system1.90e-11112
vein3.68e-119
venous blood vessel3.68e-119
venous system3.68e-119
splanchnic layer of lateral plate mesoderm6.42e-1183
epithelial tube1.75e-09117
lymphoid system1.94e-0910
segment of aorta3.24e-092
thoracic aorta3.24e-092
aorta2.51e-0821
aortic system2.51e-0821
artery1.84e-0742
arterial blood vessel1.84e-0742
arterial system1.84e-0742


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
BCL11A#53335328.36945510360714.37778126761649e-050.000779425669636206
CEBPB#105137.971147625824820.001974187055288560.0115605338865871
EP300#203336.77394172622320.003216880500103790.0168101562368828
FOS#235338.99795530889440.001372499272417130.00900618569439385
GATA2#2624312.7449317335540.0004829527704283790.00438372191819655
HDAC2#3066313.41562023662630.0004140761399857210.00392821309691786
JUN#3725312.51282919233630.0005103313992726250.00445714174683339
JUND#372736.994663941871030.002921845042734990.0157369178700531
POU5F1#54603335.4392014519062.63510205045339e-081.82377351257324e-06
RAD21#5885310.35503389545630.0009004912073565420.00667090375976095
SP1#666735.69838137814090.005403962701712170.0247537044124613
TCF7L2#6934310.77017656313730.0008003181298398380.00616313413673078
TRIM28#10155318.59052504526250.0001555969297255280.00197693281552365



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.