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Coexpression cluster:C4613

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Full id: C4613_pleomorphic_Fibroblast_mesodermal_Nucleus_Smooth_thyroid_hepatic



Phase1 CAGE Peaks

  Short description
Hg19::chr6:52441770..52441784,- p2@TRAM2
Hg19::chr6:52441791..52441804,- p3@TRAM2
Hg19::chr6:52441810..52441865,- p1@TRAM2


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


Uber Anatomy
Ontology termp-valuen
somite1.16e-1983
paraxial mesoderm1.16e-1983
presomitic mesoderm1.16e-1983
presumptive segmental plate1.16e-1983
trunk paraxial mesoderm1.16e-1983
presumptive paraxial mesoderm1.16e-1983
trunk mesenchyme1.84e-18143
dermomyotome1.08e-1770
vasculature6.90e-1779
vascular system6.90e-1779
multilaminar epithelium3.56e-1682
unilaminar epithelium6.72e-16138
trunk1.11e-14216
splanchnic layer of lateral plate mesoderm1.15e-1484
epithelial tube7.02e-14118
vessel1.18e-1369
skeletal muscle tissue1.86e-1361
striated muscle tissue1.86e-1361
myotome1.86e-1361
muscle tissue2.17e-1363
musculature2.17e-1363
musculature of body2.17e-1363
cardiovascular system4.37e-12110
circulatory system9.82e-12113
blood vessel1.26e-1160
epithelial tube open at both ends1.26e-1160
blood vasculature1.26e-1160
vascular cord1.26e-1160
mesenchyme3.47e-10238
entire embryonic mesenchyme3.47e-10238
integument6.42e-1045
integumental system6.42e-1045
artery7.04e-1042
arterial blood vessel7.04e-1042
arterial system7.04e-1042
surface structure9.76e-1095
skin of body9.57e-0940
organism subdivision1.49e-08365
systemic artery2.54e-0833
systemic arterial system2.54e-0833
organ component layer3.48e-0857


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#90536.336201576962630.003930750035764890.0191047842044513
E2F1#186934.907389214879320.008460985347239390.032747437321388
E2F6#187635.017155731697390.00791769806886330.0324128437054725
EGR1#195834.988179094810140.008056488137383440.0322318163026313
ELF1#199734.258097958807540.01295179875054610.0464724262104746
ELK4#2005210.8237877723120.01091284719516480.0402119341006885
GABPB1#255337.067683836182170.002832212825417420.0154768457133618
IRF1#365937.63716375356390.002244692747297240.0128682328375769
NFKB1#479035.488063424193840.006049381815655430.0270771605642325
REST#597839.650028716128020.001112636247114590.00770983393128985
SIN3A#2594235.408884726815140.006318961977991520.0278141387457098
TAF7#6879311.43306940492390.0006690181981945830.0054544567994726
TFAP2A#7020211.01242291536330.01054990655215560.0390343178658938
TFAP2C#7022310.80922860986020.0007916746575753130.00618597258435644
USF2#7392312.99219738506960.0004558979393427810.00422930581693203
ZBTB7A#5134137.35190930787590.002516255860282270.0140856110731639
ZNF263#1012738.221841637010680.001799043925565870.01100576080964



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.