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Coexpression cluster:C4609

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Full id: C4609_Esophageal_Urothelial_Mesothelial_bile_epidermoid_Mesenchymal_gastric



Phase1 CAGE Peaks

  Short description
Hg19::chr6:47277594..47277605,- p4@TNFRSF21
Hg19::chr6:47277620..47277631,- p3@TNFRSF21
Hg19::chr6:47277634..47277651,- p1@TNFRSF21


Enriched pathways on this co-expression clusterSummary:
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.
Analyst: Emmanuel Dimont

link to source dataset
data


No results for this coexpression

Enriched Gene Ontology terms on this co-expression clusterSummary: 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.
Analyst: Erik Arner

link to source dataset
data


No GOStat results

Enriched sample ontology terms on this co-expression clusterSummary: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. Analyst: Hideya Kawaji

links to source dataset

cell_data
uberon_data


Cell Type
Ontology termp-valuen
epithelial cell1.63e-16254
endodermal cell4.22e-1059
endo-epithelial cell4.91e-1043
embryonic cell1.18e-09248
Uber Anatomy
Ontology termp-valuen
anatomical system4.45e-30625
anatomical group1.47e-29626
multi-cellular organism5.01e-29659
embryo1.30e-24612
embryonic structure2.60e-24605
developing anatomical structure2.60e-24605
germ layer5.26e-24604
embryonic tissue5.26e-24604
presumptive structure5.26e-24604
epiblast (generic)5.26e-24604
anatomical conduit1.64e-23241
organ3.12e-20511
organism subdivision5.42e-19365
tube7.00e-19194
cell layer1.80e-18312
anatomical cluster2.06e-18286
epithelium7.54e-18309
multi-tissue structure1.49e-14347
trunk7.24e-13216
endoderm-derived structure3.75e-12169
endoderm3.75e-12169
presumptive endoderm3.75e-12169
epithelial tube9.33e-12118
organ part1.10e-11219
immaterial anatomical entity1.30e-11126
digestive system2.30e-09155
digestive tract2.30e-09155
primitive gut2.30e-09155
mesenchyme2.43e-09238
entire embryonic mesenchyme2.43e-09238
mesoderm3.49e-09448
mesoderm-derived structure3.49e-09448
presumptive mesoderm3.49e-09448
anatomical space4.40e-09104
subdivision of digestive tract1.16e-08129
endodermal part of digestive tract1.16e-08129
subdivision of trunk2.55e-08113
trunk region element4.74e-08107
trunk mesenchyme7.84e-08143
mixed endoderm/mesoderm-derived structure9.65e-08130
ectoderm-derived structure4.99e-07169
endo-epithelium5.82e-0782
central nervous system7.99e-0782
unilaminar epithelium9.14e-07138


Overrepresented TFBS (DNA) motifs on this co-expression clusterSummary: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. Analyst: Michiel de Hoon

link to source data
Novel motifs
data

Jaspar motifs
data


Novel motifs



JASPAR motifs

Motifs-log10(p-value)

{{{tfbs_overrepresentation_jaspar}}}



ENCODE TF ChIP-seq peak enrichment analysisSummary: 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.
Analyst: Erik Arner

link to source dataset

data


(#promoters = Number of promoters in this coexpression cluster that have ChIP signal of the TF)

TF#promotersEnrichmentp-valueq-value
CCNT2#90536.336201576962630.003930750035764890.0191038951549746
CEBPB#105137.971147625824820.001974187055288560.0115735123136279
CTCF#1066435.360256373075030.0064925092527670.0281135691301353
E2F1#186934.907389214879320.008460985347239390.032746223779149
E2F6#187635.017155731697390.00791769806886330.0324115732612399
EGR1#195834.988179094810140.008056488137383440.0322305816509687
ELF1#199734.258097958807540.01295179875054610.0464708296587977
FOSL2#2355316.93020060456170.0002060162053171620.00243947012098856
FOXA1#3169311.08141974938550.000734755275698670.00583862940262446
FOXA2#3170324.63046375266526.68983856509345e-050.00107671451672029
GATA2#2624312.7449317335540.0004829527704283790.00438829862456669
HDAC2#3066313.41562023662630.0004140761399857210.0039332149144128
HMGN3#932438.178547723350590.001827766942164210.010913621386581
IRF1#365937.63716375356390.002244692747297240.0128675265291716
JUN#3725312.51282919233630.0005103313992726250.00446199254990654
JUNB#3726330.61063265982113.4847716247536e-050.00068256951184854
JUND#372736.994663941871030.002921845042734990.0157596743489232
MAFF#23764356.31535648994525.59409009993116e-060.000169296197028893
MAFK#7975327.10073313782995.02195559325033e-050.000859534611936204
MAX#414936.452555509007120.003721913834265510.0187322518884321
MXI1#460139.96157162875930.001011470541259020.00723045666382964
MYC#460935.22228187160940.007020843755740150.0295868095470986
NFKB1#479035.488063424193840.006049381815655430.0270760001476488
RAD21#5885310.35503389545630.0009004912073565420.00668133000888817
RFX5#5993312.04791082719510.0005717246050312580.00486636886918171
RXRA#6256320.07461713913330.0001235730348432220.00165927541604414
SIN3A#2594235.408884726815140.006318961977991520.0278129665382441
SMC3#9126315.04493284493280.0002935825420371870.00310684639860388
SRF#6722313.79717826216780.0003806615025800190.00376262603331011
TAF7#6879311.43306940492390.0006690181981945830.00545403103592569
TCF12#6938310.63446490218640.0008313523990202070.00631826613311537
TCF7L2#6934310.77017656313730.0008003181298398380.00617041378726878
USF1#739136.361499277207960.00388404057290560.0191062744757048
USF2#7392312.99219738506960.0004558979393427810.00422855460808355
ZNF143#7702313.50087655222790.0004062804962997170.00390390364826995
ZNF263#1012738.221841637010680.001799043925565870.0110051161800606



Relative expression of the co-expression clusterSummary:Co-expression clusters are compared against FANTOM5 samples to obtain relative expression.
Analyst:NA

link to data source
data


This analysis result is provided for C0 - C305 clusters.