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Coexpression cluster:C4704

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Full id: C4704_mesenchymal_Cardiac_Smooth_Hepatocyte_myxofibrosarcoma_bronchial_gastric



Phase1 CAGE Peaks

Hg19::chr7:89783727..89783738,+p3@STEAP1
Hg19::chr7:89783740..89783755,+p2@STEAP1
Hg19::chr7:89783766..89783821,+p1@STEAP1


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><br>


Uber Anatomy
Ontology termp-valuen
unilaminar epithelium1.46e-17148
trunk mesenchyme8.74e-15122
trunk2.18e-14199
multilaminar epithelium2.30e-1483
organism subdivision2.93e-14264
mesenchyme2.94e-14160
entire embryonic mesenchyme2.94e-14160
somite5.54e-1471
presomitic mesoderm5.54e-1471
presumptive segmental plate5.54e-1471
dermomyotome5.54e-1471
trunk paraxial mesoderm5.54e-1471
paraxial mesoderm6.61e-1472
presumptive paraxial mesoderm6.61e-1472
dense mesenchyme tissue9.71e-1473
surface structure2.31e-1299
muscle tissue3.95e-1164
musculature3.95e-1164
musculature of body3.95e-1164
epithelial vesicle4.59e-1178
skeletal muscle tissue5.66e-1162
striated muscle tissue5.66e-1162
myotome5.66e-1162
multi-tissue structure1.53e-10342
splanchnic layer of lateral plate mesoderm1.92e-0983
epithelial tube2.67e-09117
multi-cellular organism4.84e-09656
artery5.14e-0942
arterial blood vessel5.14e-0942
arterial system5.14e-0942
epithelial tube open at both ends5.96e-0959
blood vessel5.96e-0959
blood vasculature5.96e-0959
vascular cord5.96e-0959
systemic artery1.03e-0833
systemic arterial system1.03e-0833
vessel2.19e-0868
integument2.71e-0846
integumental system2.71e-0846
epithelium3.14e-08306
cell layer1.04e-07309
anatomical cluster1.10e-07373
digestive system1.44e-07145
digestive tract1.44e-07145
primitive gut1.44e-07145
anatomical system3.12e-07624
anatomical group4.75e-07625
vasculature5.30e-0778
vascular system5.30e-0778
skin of body6.26e-0741
endoderm-derived structure6.93e-07160
endoderm6.93e-07160
presumptive endoderm6.93e-07160


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
BCLAF1#9774321.65264761012189.8473954032885e-050.00139488963586606
CTCF#1066435.360256373075030.0064925092527670.0281345659453854
CTCFL#140690319.74647435897440.0001298372005551160.00172366434330441
E2F1#186934.907389214879320.008460985347239390.0327765893427424
E2F6#187635.017155731697390.00791769806886330.0324331843667247
EGR1#195834.988179094810140.008056488137383440.0322503474350398
ELF1#199734.258097958807540.01295179875054610.0464979859650161
HDAC2#3066313.41562023662630.0004140761399857210.00393607881896502
MYC#460935.22228187160940.007020843755740150.0296083141936501
PAX5#507936.669565531177830.003370290999677260.0173676331827746
RAD21#5885310.35503389545630.0009004912073565420.00668703080241111
REST#597839.650028716128020.001112636247114590.00771392837310148
SETDB1#9869340.32002617801051.52461559299059e-050.000360084414102995
SIN3A#2594235.408884726815140.006318961977991520.0278293864392113
SMC3#9126315.04493284493280.0002935825420371870.00310842123964129
SP1#666735.69838137814090.005403962701712170.0247906729598576
TCF12#6938310.63446490218640.0008313523990202070.00632056585872253
YY1#752834.911170749853860.008441455341808260.0331260672744838
ZNF143#7702313.50087655222790.0004062804962997170.00390426285913196
ZNF263#1012738.221841637010680.001799043925565870.0110147935597476



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.