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Coexpression cluster:C2683: Difference between revisions

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{{Coexpression_clusters
{{Coexpression_clusters
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|full_id=C2683_pancreatic_colon_choriocarcinoma_hepatocellular_Hepatocyte_Prostate_liver
|full_id=C2683_pancreatic_colon_choriocarcinoma_hepatocellular_Hepatocyte_Prostate_liver
|id=C2683
|id=C2683

Revision as of 15:27, 12 September 2012


Full id: C2683_pancreatic_colon_choriocarcinoma_hepatocellular_Hepatocyte_Prostate_liver



Phase1 CAGE Peaks

Hg19::chr2:208630791..208630796,-p@chr2:208630791..208630796
-
Hg19::chr2:208634399..208634439,-p2@FZD5
Hg19::chr2:208634441..208634461,-p4@FZD5
Hg19::chr2:208634471..208634492,-p3@FZD5


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 cell2.96e-20254
endodermal cell1.48e-1159
Uber Anatomy
Ontology termp-valuen
endoderm-derived structure2.76e-16169
endoderm2.76e-16169
presumptive endoderm2.76e-16169
digestive system1.74e-15155
digestive tract1.74e-15155
primitive gut1.74e-15155
subdivision of digestive tract1.34e-14129
endodermal part of digestive tract1.34e-14129
trunk region element2.60e-12107
mixed endoderm/mesoderm-derived structure7.28e-12130
endo-epithelium9.91e-1282
foregut3.27e-1198
immaterial anatomical entity1.70e-09126
organ1.73e-09511
subdivision of trunk6.01e-09113
abdomen element1.31e-0855
abdominal segment element1.31e-0855
multi-cellular organism3.78e-08659
abdominal segment of trunk5.91e-0861
abdomen5.91e-0861
embryo6.54e-08612
sac1.44e-0726
adult organism2.19e-07115
primordium2.83e-07168
epithelial sac3.26e-0725
gut epithelium7.61e-0754
Disease
Ontology termp-valuen
carcinoma2.44e-22106
cell type cancer6.88e-18143
cancer1.33e-11235
disease of cellular proliferation9.42e-11239


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
BHLHE40#8553333.65386016023314.35025573591721e-050.000775185734180955
CCNT2#90546.336201576962630.0006203100587215640.00512941902001753
CTCFL#140690314.80985576923080.0004996291767563340.00441013958682004
EBF1#187936.679850134926750.005184294118278910.0240555577314258
ESR1#2099323.07645247211590.0001339105244968570.00175829535679246
ETS1#211337.296570691651750.00400857377511390.0192085999770186
FOSL2#2355312.69765045342130.000787568572975710.00616773201807214
FOXA1#316938.311064812039090.002740138182109850.0150382181608707
HDAC2#3066310.06171517746970.00156372754474740.00992610107857981
HNF4A#3172317.34921777221530.0003125641557482750.00321582975689036
HNF4G#3174321.56506689483510.0001638032421292610.00203708583052368
IRF1#365935.727872815172930.008097114790333330.0320141802607466
NFYB#4801312.56984494015230.000811456397697350.00619093394105585
NR3C1#2908311.22976749837980.001131672068063850.00775580412865154
PAX5#507935.002174148383370.01196533174786410.0435098806592798
POU5F1#5460183.85980036297640.01187154239091560.0432426065766195
RAD21#588537.766275421592250.0033411193858720.0172709942358487
RXRA#6256315.055962854350.0004758307997303580.00433944227148436
SMC3#9126311.28369963369960.001115802366868050.00765809840266365
TFAP2A#7020312.38897577978370.000846941303588430.00638194103935585
TFAP2C#702238.106921457395170.002947011739866440.0157184494714219
USF1#739134.771124457905970.01370465887188020.0483188463952566
ZBTB7A#5134135.513931980906920.009038352821081090.0342522054603174



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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