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Coexpression cluster:C3424

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Full id: C3424_skeletal_tongue_diaphragm_mesenchymal_Fibroblast_basal_smooth



Phase1 CAGE Peaks

Hg19::chr14:35183771..35183784,-p4@CFL2
Hg19::chr14:35183785..35183826,-p1@CFL2
Hg19::chr14:35183837..35183867,-p2@CFL2


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
multi-tissue structure1.11e-22342
cell layer4.78e-19309
epithelium2.24e-18306
anatomical cluster1.33e-17373
structure with developmental contribution from neural crest1.43e-15132
mesenchyme1.50e-14160
entire embryonic mesenchyme1.50e-14160
dense mesenchyme tissue1.67e-1473
paraxial mesoderm2.50e-1472
presumptive paraxial mesoderm2.50e-1472
somite3.13e-1471
presomitic mesoderm3.13e-1471
presumptive segmental plate3.13e-1471
dermomyotome3.13e-1471
trunk paraxial mesoderm3.13e-1471
trunk mesenchyme1.88e-13122
multi-cellular organism6.01e-13656
epithelial vesicle1.99e-1278
muscle tissue3.04e-1264
musculature3.04e-1264
musculature of body3.04e-1264
skeletal muscle tissue6.94e-1262
striated muscle tissue6.94e-1262
myotome6.94e-1262
anatomical conduit7.87e-12240
anatomical system9.62e-12624
unilaminar epithelium1.02e-11148
anatomical group1.43e-11625
organism subdivision2.72e-11264
multilaminar epithelium4.45e-1183
tube4.74e-10192
adult organism7.87e-10114
trunk1.96e-09199
ectoderm-derived structure4.64e-09171
ectoderm4.64e-09171
presumptive ectoderm4.64e-09171
neural plate8.14e-0982
presumptive neural plate8.14e-0982
organ system subdivision1.07e-08223
nervous system1.72e-0889
neurectoderm2.35e-0886
neural tube9.34e-0856
neural rod9.34e-0856
future spinal cord9.34e-0856
neural keel9.34e-0856
brain1.16e-0768
future brain1.16e-0768
surface structure1.23e-0799
central nervous system1.60e-0781
regional part of nervous system4.19e-0753
regional part of brain4.19e-0753
ecto-epithelium8.14e-07104


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
ATF3#467322.46317452600878.81932387510763e-050.0012945627072275
BHLHE40#8553344.87181354697741.10603738662898e-050.000284165900669481
CCNT2#90536.336201576962630.003930750035764890.0189600777288587
E2F1#186934.907389214879320.008460985347239390.0324337254057748
E2F6#187635.017155731697390.00791769806886330.0321232409530733
EBF1#187938.9064668465690.00141523283560980.00913676838216309
EGR1#195834.988179094810140.008056488137383440.0319721687342854
HDAC2#3066313.41562023662630.0004140761399857210.0039055087134443
HNF4G#3174328.75342252644684.20470658818262e-050.000755826766545963
JUND#372736.994663941871030.002921845042734990.0156425350839758
MAX#414936.452555509007120.003721913834265510.0186129553216269
MYC#460935.22228187160940.007020843755740150.0293793533538643
NANOG#79923329.24477848101273.99627955670032e-050.000736227625017155
RXRA#6256320.07461713913330.0001235730348432220.0016503637066485
SIN3A#2594235.408884726815140.006318961977991520.0275931793293246
TAF7#6879311.43306940492390.0006690181981945830.0054168223584188
TFAP2A#7020316.5186343730450.0002218033880766340.00247726703532623
TFAP2C#7022310.80922860986020.0007916746575753130.00614094693720351
USF1#739136.361499277207960.00388404057290560.0189882185738748
USF2#7392312.99219738506960.0004558979393427810.00420986073271625
YY1#752834.911170749853860.008441455341808260.0328593795916181
ZEB1#6935316.88843201754390.0002075486917327580.00242327309288737
ZNF143#7702313.50087655222790.0004062804962997170.00388318191205693



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.