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Coexpression cluster:C3433: Difference between revisions

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|full_id=C3433_teratocarcinoma_Saos2_signet_rectal_tubular_gastric_Wilms
|full_id=C3433_teratocarcinoma_Saos2_signet_rectal_tubular_gastric_Wilms
|id=C3433
|id=C3433
|ontology_enrichment_celltype=CL:0000213!1.31e-19!57;CL:0000215!1.31e-19!57;CL:0002078!1.49e-15!44;CL:0002139!1.81e-12!24;CL:0000115!2.44e-12!35;CL:0000222!4.47e-12!119;CL:0000066!9.45e-10!254;CL:0000071!1.89e-09!18;CL:0002546!1.89e-09!18;CL:0000076!7.65e-09!62;CL:1000413!2.31e-07!9;CL:0002321!2.44e-07!248;CL:0000077!4.27e-07!19;CL:0000220!5.98e-07!246
|ontology_enrichment_disease=
|ontology_enrichment_uberon=UBERON:0000477!9.35e-20!286;UBERON:0004111!1.34e-19!241;UBERON:0000119!9.80e-18!312;UBERON:0000483!1.73e-17!309;UBERON:0000481!6.57e-16!347;UBERON:0000025!4.07e-14!194;UBERON:0003914!1.19e-13!118;UBERON:0006914!1.32e-12!25;UBERON:0000487!3.72e-11!22;UBERON:0001986!1.89e-09!18;UBERON:0004638!1.89e-09!18;UBERON:0004852!1.89e-09!18;UBERON:0003064!3.24e-09!37;UBERON:0002100!5.14e-09!216;UBERON:0001007!7.61e-09!155;UBERON:0001555!7.61e-09!155;UBERON:0007026!7.61e-09!155;UBERON:0000466!1.13e-08!126;UBERON:0003104!1.25e-08!238;UBERON:0009142!1.25e-08!238;UBERON:0000490!1.74e-08!138;UBERON:0009569!2.03e-08!113;UBERON:0004921!4.21e-08!129;UBERON:0004185!4.21e-08!129;UBERON:0000058!4.57e-08!26;UBERON:0001048!4.94e-08!168;UBERON:0002049!5.12e-08!79;UBERON:0007798!5.12e-08!79;UBERON:0000475!8.33e-08!365;UBERON:0000064!9.67e-08!219;UBERON:0003103!1.09e-07!69;UBERON:0000468!1.76e-07!659;UBERON:0003915!2.31e-07!9;UBERON:0004700!2.31e-07!9;UBERON:0001917!2.31e-07!9;UBERON:0005256!3.20e-07!143;UBERON:0004119!5.39e-07!169;UBERON:0000925!5.39e-07!169;UBERON:0006595!5.39e-07!169;UBERON:0005177!5.70e-07!107;UBERON:0004872!8.92e-07!84;UBERON:0005172!9.17e-07!55;UBERON:0005173!9.17e-07!55
}}
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Revision as of 14:36, 21 May 2012


Full id: C3433_teratocarcinoma_Saos2_signet_rectal_tubular_gastric_Wilms



Phase1 CAGE Peaks

Hg19::chr14:54423434..54423446,-p6@BMP4
Hg19::chr14:54423459..54423483,-p4@BMP4
Hg19::chr14:54423533..54423552,-p1@BMP4


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
anatomical cluster9.35e-20286
anatomical conduit1.34e-19241
cell layer9.80e-18312
epithelium1.73e-17309
multi-tissue structure6.57e-16347
tube4.07e-14194
epithelial tube1.19e-13118
squamous epithelium1.32e-1225
simple squamous epithelium3.72e-1122
endothelium1.89e-0918
blood vessel endothelium1.89e-0918
cardiovascular system endothelium1.89e-0918
intermediate mesoderm3.24e-0937
trunk5.14e-09216
digestive system7.61e-09155
digestive tract7.61e-09155
primitive gut7.61e-09155
immaterial anatomical entity1.13e-08126
mesenchyme1.25e-08238
entire embryonic mesenchyme1.25e-08238
unilaminar epithelium1.74e-08138
subdivision of trunk2.03e-08113
subdivision of digestive tract4.21e-08129
endodermal part of digestive tract4.21e-08129
duct4.57e-0826
primordium4.94e-08168
vasculature5.12e-0879
vascular system5.12e-0879
organism subdivision8.33e-08365
organ part9.67e-08219
compound organ1.09e-0769
multi-cellular organism1.76e-07659
endothelial tube2.31e-079
arterial system endothelium2.31e-079
endothelium of artery2.31e-079
trunk mesenchyme3.20e-07143
endoderm-derived structure5.39e-07169
endoderm5.39e-07169
presumptive endoderm5.39e-07169
trunk region element5.70e-07107
splanchnic layer of lateral plate mesoderm8.92e-0784
abdomen element9.17e-0755
abdominal segment element9.17e-0755


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.

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