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Coexpression cluster:C1169: Difference between revisions

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|ontology_enrichment_uberon=UBERON:0000365!6.71e-31!5;UBERON:0005910!9.95e-26!6;UBERON:0001949!7.60e-19!3;UBERON:0001255!1.29e-12!2;UBERON:0001556!1.29e-12!2;UBERON:0003350!3.39e-12!8;UBERON:0003729!2.98e-11!13;UBERON:0006554!6.22e-11!47;UBERON:0001008!1.14e-10!48;UBERON:0000344!4.11e-10!20;UBERON:0004119!1.99e-09!160;UBERON:0000925!1.99e-09!160;UBERON:0006595!1.99e-09!160;UBERON:0000161!2.43e-09!36;UBERON:0004815!6.33e-09!3;UBERON:0002031!6.33e-09!3;UBERON:0003102!7.08e-09!99;UBERON:0005911!2.66e-08!82;UBERON:0001828!2.29e-07!8;UBERON:0000997!3.62e-07!1;UBERON:0005056!3.62e-07!1;UBERON:0001708!4.22e-07!4;UBERON:0008895!4.22e-07!4;UBERON:0004645!4.34e-07!1;UBERON:0001256!4.34e-07!1;UBERON:0001259!4.34e-07!1;UBERON:0006834!4.89e-07!1;UBERON:0000162!7.18e-07!14;UBERON:0001353!7.18e-07!14;UBERON:0000163!7.18e-07!14;UBERON:0006866!7.18e-07!14;UBERON:0000164!7.18e-07!14;UBERON:0000931!7.18e-07!14
|ontology_enrichment_uberon=UBERON:0000365!6.71e-31!5;UBERON:0005910!9.95e-26!6;UBERON:0001949!7.60e-19!3;UBERON:0001255!1.29e-12!2;UBERON:0001556!1.29e-12!2;UBERON:0003350!3.39e-12!8;UBERON:0003729!2.98e-11!13;UBERON:0006554!6.22e-11!47;UBERON:0001008!1.14e-10!48;UBERON:0000344!4.11e-10!20;UBERON:0004119!1.99e-09!160;UBERON:0000925!1.99e-09!160;UBERON:0006595!1.99e-09!160;UBERON:0000161!2.43e-09!36;UBERON:0004815!6.33e-09!3;UBERON:0002031!6.33e-09!3;UBERON:0003102!7.08e-09!99;UBERON:0005911!2.66e-08!82;UBERON:0001828!2.29e-07!8;UBERON:0000997!3.62e-07!1;UBERON:0005056!3.62e-07!1;UBERON:0001708!4.22e-07!4;UBERON:0008895!4.22e-07!4;UBERON:0004645!4.34e-07!1;UBERON:0001256!4.34e-07!1;UBERON:0001259!4.34e-07!1;UBERON:0006834!4.89e-07!1;UBERON:0000162!7.18e-07!14;UBERON:0001353!7.18e-07!14;UBERON:0000163!7.18e-07!14;UBERON:0006866!7.18e-07!14;UBERON:0000164!7.18e-07!14;UBERON:0000931!7.18e-07!14
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|tfbs_overrepresentation_for_novel_motifs=0.392069,0.465735,0.384703,0.529489,0.343148,0.52784,0.604235,0.226729,0.224331,0.0544999,0.497563,0.647852,0.184039,0.592674,0.905441,0.956905,0.827563,1.43406,0.19568,0.66776,0.384762,0.0646572,0.520063,0.338096,0.430372,0.670692,0.164928,0.517892,0.346214,0.459534,0.475674,0.864517,0.257226,0.546594,0.309012,0.232776,0.305874,0.529001,0.773034,0.207499,0.307642,0.459366,0.0729319,0.340293,0.265117,0.415364,0.60533,0.486696,0.0670664,0.346342,0.684981,0.617179,0.373994,0.941629,1.09491,0.595623,0.350547,0.562713,0.459282,0.561701,0.905643,0.60771,0.224801,0.799729,0.625758,0.76514,1.18348,1.55228,0.854088,1.38987,0.4462,1.22295,0.115253,1.0929,0.179863,0.168304,0.156354,0.782748,0.850825,0.424224,0.580264,0.798651,0.625403,0.649554,1.04131,0.0324537,0.097572,0.88003,0.711163,1.65172,1.27705,1.01423,0.881388,0.26423,0.343884,0.277058,0.566252,0.924148,0.715799,0.132387,0.28424,0.875714,0.918549,0.831244,0.753567,0.493026,0.815341,0.589207,0.43012,0.327379,0.395884,0.915771,0.379203,0.507004,1.22894,0.821533,0.358137,0.474472,0.762789,0.26701,1.0846,0.708722,0.525076,0.636741,1.33983,0.783512,0.597853,0.886402,1.12733,0.27799,1.01492,1.20354,1.14174,0.633392,1.28996,0.854586,0.469685,1.28879,1.24743,2.10682,1.70417,1.21002,0.59959,0.920609,0.755332,1.36465,0.738579,1.94751,0.456039,0.26104,0.106334,0.0685123,1.0153,0.216774,0.607223,1.42052,0.694887,0.329354,0.430431,0.401655,1.2088,0.996724,0.850033,0.404861,0.7715,0.624608,0.24928,0.602897,0.00626991
}}
}}

Revision as of 14:43, 26 November 2012


Full id: C1169_Urothelial_meningioma_medulloblastoma_Prostate_fibrosarcoma_Anulus_Nucleus



Phase1 CAGE Peaks

Hg19::chr12:47472578..47472594,-p14@AMIGO2
Hg19::chr12:47472684..47472703,-p12@AMIGO2
Hg19::chr18:26736753..26736764,+p@chr18:26736753..26736764
+
Hg19::chr18:43307294..43307345,+p@chr18:43307294..43307345
+
Hg19::chr1:183212642..183212654,+p@chr1:183212642..183212654
+
Hg19::chr21:39628993..39628998,+p25@KCNJ15
Hg19::chr8:141728731..141728740,-p38@PTK2


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:0007157heterophilic cell adhesion0.0478276194456524
GO:0007172signal complex assembly0.0478276194456524
GO:0005886plasma membrane0.0478276194456524
GO:0042169SH2 domain binding0.0478276194456524
GO:0005242inward rectifier potassium channel activity0.0478276194456524
GO:0005925focal adhesion0.0478276194456524
GO:0005924cell-substrate adherens junction0.0478276194456524
GO:0004715non-membrane spanning protein tyrosine kinase activity0.0478276194456524
GO:0030055cell-matrix junction0.0478276194456524



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>disease_data<br>


Cell Type
Ontology termp-valuen
transitional epithelial cell1.50e-254
urothelial cell1.50e-254
gingival epithelial cell7.60e-193
endo-epithelial cell3.80e-1842
respiratory epithelial cell3.89e-1613
epithelial cell4.19e-13253
endodermal cell1.70e-1258
general ecto-epithelial cell1.39e-1014
stratified squamous epithelial cell2.92e-096
keratin accumulating cell2.92e-096
stratified epithelial cell2.92e-096
keratinizing barrier epithelial cell2.92e-096
epithelial fate stem cell2.92e-096
stratified epithelial stem cell2.92e-096
surface ectodermal cell2.92e-096
epithelial cell of Malassez3.34e-093
bronchial epithelial cell6.33e-093
epithelial cell of alimentary canal3.14e-0720
buccal mucosa cell4.08e-071
endothelial cell of viscerocranial mucosa4.08e-071
keratinized cell of the oral mucosa4.08e-071
bladder cell4.34e-071
lower urinary tract cell4.34e-071
Uber Anatomy
Ontology termp-valuen
urothelium6.71e-315
transitional epithelium9.95e-266
gingival epithelium7.60e-193
urinary bladder1.29e-122
lower urinary tract1.29e-122
epithelium of mucosa3.39e-128
mouth mucosa2.98e-1113
urinary system structure6.22e-1147
renal system1.14e-1048
mucosa4.11e-1020
endoderm-derived structure1.99e-09160
endoderm1.99e-09160
presumptive endoderm1.99e-09160
orifice2.43e-0936
lower respiratory tract epithelium6.33e-093
epithelium of bronchus6.33e-093
surface structure7.08e-0999
endo-epithelium2.66e-0882
gingiva2.29e-078
mammalian vulva3.62e-071
external female genitalia3.62e-071
jaw skeleton4.22e-074
splanchnocranium4.22e-074
urinary bladder urothelium4.34e-071
wall of urinary bladder4.34e-071
mucosa of urinary bladder4.34e-071
uterus or analog4.89e-071
cloaca7.18e-0714
anal region7.18e-0714
embryonic cloaca7.18e-0714
terminal part of digestive tract7.18e-0714
primitive urogenital sinus7.18e-0714
proctodeum7.18e-0714
Disease
Ontology termp-valuen
squamous cell carcinoma6.43e-0714


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


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.