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Coexpression cluster:C2540: Difference between revisions

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{{Coexpression_clusters
{{Coexpression_clusters
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|full_id=C2540_small_neuroblastoma_nonsmall_Urothelial_colon_anaplastic_Smooth
|full_id=C2540_small_neuroblastoma_nonsmall_Urothelial_colon_anaplastic_Smooth
|id=C2540
|id=C2540

Revision as of 15:17, 12 September 2012


Full id: C2540_small_neuroblastoma_nonsmall_Urothelial_colon_anaplastic_Smooth



Phase1 CAGE Peaks

Hg19::chr1:165796753..165796776,+p5@UCK2
Hg19::chr1:165796782..165796803,+p2@UCK2
Hg19::chr1:165796811..165796860,+p1@UCK2
Hg19::chr1:165796870..165796886,+p4@UCK2


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>disease_data<br>


Cell Type
Ontology termp-valuen
epithelial cell5.93e-32254
animal cell3.78e-23679
eukaryotic cell3.78e-23679
embryonic cell9.36e-23248
squamous epithelial cell8.83e-1162
non-terminally differentiated cell1.41e-10180
native cell1.56e-10722
mesodermal cell4.31e-09119
endo-epithelial cell7.55e-0843
endodermal cell2.31e-0759
Uber Anatomy
Ontology termp-valuen
mesenchyme1.01e-14238
entire embryonic mesenchyme1.01e-14238
trunk mesenchyme4.01e-09143
endoderm-derived structure6.87e-09169
endoderm6.87e-09169
presumptive endoderm6.87e-09169
trunk7.57e-09216
cell layer1.04e-08312
epithelium3.74e-08309
multilaminar epithelium5.89e-0882
unilaminar epithelium8.05e-08138
epithelial tube9.02e-08118
multi-tissue structure1.21e-07347
respiratory primordium1.22e-0738
endoderm of foregut1.22e-0738
segment of respiratory tract1.61e-0746
larynx2.21e-079
respiratory system2.96e-0772
respiratory tract7.26e-0753
digestive system9.51e-07155
digestive tract9.51e-07155
primitive gut9.51e-07155
Disease
Ontology termp-valuen
cancer9.56e-28235
disease of cellular proliferation2.57e-27239
cell type cancer7.18e-18143
carcinoma2.30e-14106
organ system cancer1.25e-10137


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
CCNT2#90546.336201576962630.0006203100587215640.00512333429994634
CTCF#1066445.360256373075030.001211145381643620.00817599460367645
CTCFL#140690419.74647435897446.5732084880439e-060.000192999528052521
E2F1#186944.907389214879320.001724022357361790.0106510009453125
E2F6#187645.017155731697390.00157802193473060.00997138388439793
EGR1#195844.988179094810140.001615011500076050.0101474062120348
ELF1#199744.258097958807540.003041525565781240.0160951504136921
GABPB1#255347.067683836182170.0004006876864423170.00390367735861466
HEY1#2346244.040111043105710.00375304636917980.0186162151389584
NFYA#4800418.42558069983058.67100748407158e-060.000234548394361293
NFYB#4801416.75979325353651.26678572070404e-050.000311518327959994
NR2C2#7182432.61461090524098.82887529809196e-073.81971378317078e-05
SMARCB1#6598418.25271578115749.00423392720929e-060.000241560027517033
TAF1#687243.343046285745290.008005664898701650.0322396713332113
TAF7#6879411.43306940492395.85061525419808e-050.000969584904051402
TAL1#6886214.93430833872010.006428077577888070.0279492920131995
TBP#690843.706770687096390.005296377814784350.0244366673704834
USF1#739146.361499277207960.0006105011399140830.00508129809941719



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.