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Coexpression cluster:C2221

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Full id: C2221_Mesenchymal_Fibroblast_Keratocytes_Keratinocyte_Osteoblast_mesenchymal_Hepatocyte



Phase1 CAGE Peaks

  Short description
Hg19::chr12:57623876..57623891,+ p5@SHMT2
Hg19::chr12:57623907..57623961,+ p2@SHMT2
Hg19::chr12:57623963..57623989,+ p4@SHMT2
Hg19::chr12:57623992..57624003,+ p9@SHMT2


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
animal cell1.09e-30679
eukaryotic cell1.09e-30679
somatic cell2.49e-19588
native cell2.07e-17722
fibroblast7.41e-1576
embryonic cell9.83e-15250
mesodermal cell9.56e-13121
epithelial cell8.95e-11253
non-terminally differentiated cell6.28e-09106
smooth muscle cell6.59e-0943
smooth muscle myoblast6.59e-0943
contractile cell7.20e-0959
muscle precursor cell8.95e-0958
myoblast8.95e-0958
multi-potent skeletal muscle stem cell8.95e-0958
vascular associated smooth muscle cell1.15e-0832
muscle cell1.18e-0855
Uber Anatomy
Ontology termp-valuen
epithelial tube7.31e-13117
unilaminar epithelium5.45e-12148
splanchnic layer of lateral plate mesoderm6.97e-1283
epithelial tube open at both ends2.83e-1159
blood vessel2.83e-1159
blood vasculature2.83e-1159
vascular cord2.83e-1159
vessel3.90e-1168
artery4.11e-1142
arterial blood vessel4.11e-1142
arterial system4.11e-1142
vasculature8.82e-1178
vascular system8.82e-1178
trunk9.60e-11199
organism subdivision4.88e-10264
systemic artery1.85e-0833
systemic arterial system1.85e-0833
trunk mesenchyme8.91e-08122
multilaminar epithelium2.80e-0783
cardiovascular system4.13e-07109
somite5.39e-0771
presomitic mesoderm5.39e-0771
presumptive segmental plate5.39e-0771
dermomyotome5.39e-0771
trunk paraxial mesoderm5.39e-0771
dense mesenchyme tissue6.24e-0773
epithelial vesicle6.60e-0778
skeletal muscle tissue8.65e-0762
striated muscle tissue8.65e-0762
myotome8.65e-0762


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
ATF3#467422.46317452600873.92475754624726e-060.000127178949231312
CEBPB#105147.971147625824820.0002476385788090830.00267651097301478
E2F1#186944.907389214879320.001724022357361790.0106315051358354
E2F6#187645.017155731697390.00157802193473060.00995512128307635
HEY1#2346244.040111043105710.00375304636917980.0185650741131421
JUND#372746.994663941871030.000417684217818580.00391058019047554
MAX#414946.452555509007120.0005767613195645490.00484721778820326
MXI1#460149.96157162875930.0001015224754950450.00142168219606154
MYC#460945.22228187160940.001344309395272740.00886185248582272
NFKB1#479045.488063424193840.001102199566301980.00766957295656022
SIN3A#2594245.408884726815140.001168172384885160.0079480622609134
TAF1#687243.343046285745290.008005664898701650.0321454685257786
TBP#690843.706770687096390.005296377814784350.0243634779157092
TFAP2A#7020416.5186343730451.34240829060362e-050.000326121841038268
TFAP2C#7022410.80922860986027.32289634782688e-050.00114404782598458
USF1#739146.361499277207960.0006105011399140830.00507159788032826
USF2#7392412.99219738506963.50833029870167e-050.000680294296446535
ZBTB7A#5134147.35190930787590.000342223540015990.00346097456141473



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.