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Coexpression cluster:C4173

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Full id: C4173_Smooth_mesenchymal_amniotic_tenocyte_ductus_seminal_Synoviocyte



Phase1 CAGE Peaks

Hg19::chr2:20251339..20251367,-p3@LAPTM4A
Hg19::chr2:20251371..20251400,-p1@LAPTM4A
Hg19::chr2:20251406..20251451,-p2@LAPTM4A


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>


Cell Type
Ontology termp-valuen
non-terminally differentiated cell2.53e-18180
fibroblast5.53e-1275
somatic cell2.09e-11591
multi fate stem cell6.29e-10430
stem cell3.62e-09444
somatic stem cell4.10e-09436
contractile cell3.71e-0859
mesodermal cell4.51e-08119
muscle precursor cell6.23e-0857
myoblast6.23e-0857
multi-potent skeletal muscle stem cell6.23e-0857
fat cell1.10e-0715
stromal cell1.55e-0727
muscle cell3.12e-0754
animal cell5.20e-07679
eukaryotic cell5.20e-07679
Uber Anatomy
Ontology termp-valuen
multi-cellular organism8.27e-14659
mesoderm1.24e-13448
mesoderm-derived structure1.24e-13448
presumptive mesoderm1.24e-13448
trunk mesenchyme1.20e-09143
anatomical system1.92e-09625
anatomical group3.61e-09626
extraembryonic membrane4.31e-0914
membranous layer4.31e-0914
somite1.15e-0783
paraxial mesoderm1.15e-0783
presomitic mesoderm1.15e-0783
presumptive segmental plate1.15e-0783
trunk paraxial mesoderm1.15e-0783
presumptive paraxial mesoderm1.15e-0783
trunk2.18e-07216
muscle tissue2.31e-0763
musculature2.31e-0763
musculature of body2.31e-0763
skeletal muscle tissue2.70e-0761
striated muscle tissue2.70e-0761
myotome2.70e-0761
reproductive structure3.61e-0759
reproductive system3.61e-0759
extraembryonic structure6.26e-0724
multilaminar epithelium6.66e-0782
organ8.58e-07511
musculoskeletal system9.87e-07167


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
BHLHE40#8553344.87181354697741.10603738662898e-050.000285077587912498
CHD2#1106310.34402283411690.0009033701102746880.00661574019682899
E2F6#187635.017155731697390.00791769806886330.0323102593917874
EBF1#187938.9064668465690.00141523283560980.00916964465030413
EGR1#195834.988179094810140.008056488137383440.0321357966841152
ELF1#199734.258097958807540.01295179875054610.046346635705759
FOS#235338.99795530889440.001372499272417130.00899375401631149
GATA1#2623313.56030814380040.0004009615963782630.00388604567224846
HNF4A#3172215.42152690863580.005444210486686610.0246825793982923
IRF1#365937.63716375356390.002244692747297240.012837931429548
IRF3#3661346.98195221148969.63568551583244e-060.000253806143653978
JUND#372736.994663941871030.002921845042734990.0157101819613982
MAX#414936.452555509007120.003721913834265510.0186971120219748
MXI1#460139.96157162875930.001011470541259020.007213669206402
MYC#460935.22228187160940.007020843755740150.0295165405766744
NFYA#4800318.42558069983050.0001598135507814160.00199985231608679
NFYB#4801316.75979325353650.0002123649923296180.00246298583386041
NRF1#4899312.21027944771090.0005492172401020010.00472057438392008
PBX3#5090321.91451268674419.49854535978121e-050.00136943481340446
POU2F2#545239.106124057742520.001324165192682130.0088350149210074
PPARGC1A#108913350.0511363636362.31814761783079e-081.63584472336912e-06
RFX5#5993312.04791082719510.0005717246050312580.00485489438367831
SIN3A#2594235.408884726815140.006318961977991520.0277451471461976
SMARCB1#6598318.25271578115740.000164397760679890.0020345464779769
SP1#666735.69838137814090.005403962701712170.0247071076743036
SP2#6668326.15353049384465.58768218891694e-050.000941548790139232
SREBF1#6720347.00584944048839.62099323994382e-060.00025502713527576
STAT1#6772320.70658749719920.0001125992441046670.00155060027097143
STAT3#6774310.51946499715420.0008589184530415310.00643782003137681
THAP1#55145331.36914460285133.23800758564397e-050.000648091748250423
USF1#739136.361499277207960.00388404057290560.0190757260001734



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.