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{{Coexpression_clusters
{{Coexpression_clusters
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|full_id=C3973_bronchogenic_chorionic_hepatoblastoma_small_testicular_rectum_adenocarcinoma
|full_id=C3973_bronchogenic_chorionic_hepatoblastoma_small_testicular_rectum_adenocarcinoma
|id=C3973
|id=C3973

Revision as of 16:59, 12 September 2012


Full id: C3973_bronchogenic_chorionic_hepatoblastoma_small_testicular_rectum_adenocarcinoma



Phase1 CAGE Peaks

Hg19::chr1:3371210..3371219,+p9@ARHGEF16
Hg19::chr1:3371222..3371243,+p1@ARHGEF16
Hg19::chr1:3371261..3371278,+p4@ARHGEF16


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 cell3.32e-36254
endodermal cell1.52e-1259
endo-epithelial cell4.31e-1043
epithelial cell of lung3.94e-0719
Uber Anatomy
Ontology termp-valuen
endoderm-derived structure2.39e-22169
endoderm2.39e-22169
presumptive endoderm2.39e-22169
subdivision of digestive tract1.36e-20129
endodermal part of digestive tract1.36e-20129
digestive system2.55e-20155
digestive tract2.55e-20155
primitive gut2.55e-20155
mixed endoderm/mesoderm-derived structure7.16e-17130
foregut2.38e-1598
trunk region element6.57e-14107
immaterial anatomical entity4.74e-13126
respiratory tract2.44e-1253
respiratory system6.35e-1272
respiratory primordium1.48e-1138
endoderm of foregut1.48e-1138
segment of respiratory tract4.75e-1146
anatomical space7.13e-11104
endo-epithelium1.52e-1082
organ part3.44e-10219
organ segment2.02e-0997
multi-tissue structure5.68e-09347
organ6.92e-09511
renal system9.10e-0945
primordium1.29e-08168
subdivision of trunk1.67e-08113
urinary system structure2.07e-0844
abdomen element6.69e-0855
abdominal segment element6.69e-0855
mesenchyme1.05e-07238
entire embryonic mesenchyme1.05e-07238
gastrointestinal system1.62e-0735
cavitated compound organ2.36e-0732
respiratory tract epithelium3.94e-0719
lung epithelium3.94e-0719
larynx5.52e-079
lung7.56e-0722
respiratory tube7.56e-0722
respiration organ7.56e-0722
pair of lungs7.56e-0722
lung primordium7.56e-0722
lung bud7.56e-0722
kidney8.60e-0727
kidney mesenchyme8.60e-0727
kidney rudiment8.60e-0727
kidney field8.60e-0727
epithelial bud9.78e-0737
Disease
Ontology termp-valuen
carcinoma9.18e-37106
cell type cancer7.18e-29143
cancer1.94e-16235
disease of cellular proliferation1.38e-15239
adenocarcinoma1.92e-0925
squamous cell carcinoma5.25e-0814


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
CTCF#1066435.360256373075030.0064925092527670.0279709254124962
CTCFL#140690319.74647435897440.0001298372005551160.00171929344348622
E2F1#186934.907389214879320.008460985347239390.032567605818757
E2F6#187635.017155731697390.00791769806886330.0322585811271754
EGR1#195834.988179094810140.008056488137383440.0320953450022959
RAD21#5885310.35503389545630.0009004912073565420.00664591910148469
SMC3#9126315.04493284493280.0002935825420371870.00309336835228226
USF1#739136.361499277207960.00388404057290560.0190479579918148
USF2#7392312.99219738506960.0004558979393427810.00421993484773737
ZBTB7A#5134137.35190930787590.002516255860282270.0140359582220808
ZNF263#1012738.221841637010680.001799043925565870.0109525123020795



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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