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Coexpression cluster:C3426

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Full id: C3426_bronchioalveolar_anaplastic_astrocytoma_small_somatostatinoma_large_prostate



Phase1 CAGE Peaks

Hg19::chr14:36989892..36989908,-p9@NKX2-1
Hg19::chr14:36989913..36989931,-p6@NKX2-1
Hg19::chr14:36989940..36989957,-p2@NKX2-1


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
endo-epithelial cell4.07e-0843
epithelial cell of lung2.15e-0719
respiratory epithelial cell2.21e-0713
Uber Anatomy
Ontology termp-valuen
respiratory primordium1.66e-2138
endoderm of foregut1.66e-2138
respiratory tract9.51e-2153
respiratory system6.03e-1872
endoderm-derived structure2.15e-13169
endoderm2.15e-13169
presumptive endoderm2.15e-13169
larynx4.81e-139
segment of respiratory tract7.30e-1346
digestive system1.95e-12155
digestive tract1.95e-12155
primitive gut1.95e-12155
lung3.45e-1122
respiratory tube3.45e-1122
respiration organ3.45e-1122
pair of lungs3.45e-1122
lung primordium3.45e-1122
lung bud3.45e-1122
subdivision of digestive tract7.39e-11129
endodermal part of digestive tract7.39e-11129
foregut2.80e-1098
regional part of forebrain8.21e-1041
forebrain8.21e-1041
future forebrain8.21e-1041
mixed endoderm/mesoderm-derived structure1.82e-09130
anterior neural tube1.82e-0942
thoracic cavity element1.91e-0934
thoracic cavity1.91e-0934
thoracic segment organ4.71e-0935
telencephalic nucleus9.89e-097
regional part of telencephalon8.07e-0833
telencephalon1.72e-0734
corpus striatum1.98e-074
striatum1.98e-074
ventral part of telencephalon1.98e-074
future corpus striatum1.98e-074
respiratory tract epithelium2.15e-0719
lung epithelium2.15e-0719
epithelial bud2.24e-0737
cerebral hemisphere4.00e-0732
organ part4.18e-07219
endo-epithelium8.61e-0782
Disease
Ontology termp-valuen
carcinoma6.73e-18106
squamous cell carcinoma1.10e-1214
cell type cancer1.30e-12143
cancer1.98e-11235
disease of cellular proliferation7.26e-11239
respiratory system cancer1.21e-0716
lung carcinoma8.97e-079


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#1066435.360256373075030.0064925092527670.0278835090817392
CTCFL#140690319.74647435897440.0001298372005551160.0017142942337264
MYC#460935.22228187160940.007020843755740150.0293805305527806
RFX5#5993312.04791082719510.0005717246050312580.00483758778456287
SUZ12#23512350.11578091106297.93834897779404e-060.000221795941383583



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.