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Coexpression cluster:C4324: Difference between revisions

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{{Coexpression_clusters
{{Coexpression_clusters
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|full_id=C4324_Endothelial_Lymphatic_Hepatic_Smooth_Neutrophils_adipose_breast
|full_id=C4324_Endothelial_Lymphatic_Hepatic_Smooth_Neutrophils_adipose_breast
|id=C4324
|id=C4324

Revision as of 17:23, 12 September 2012


Full id: C4324_Endothelial_Lymphatic_Hepatic_Smooth_Neutrophils_adipose_breast



Phase1 CAGE Peaks

Hg19::chr3:30647997..30648010,+p4@TGFBR2
Hg19::chr3:30648011..30648061,+p2@TGFBR2
Hg19::chr3:30648066..30648167,+p1@TGFBR2


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
circulatory system1.65e-29113
cardiovascular system3.41e-28110
vasculature2.02e-2479
vascular system2.02e-2479
vessel1.26e-2369
splanchnic layer of lateral plate mesoderm4.32e-2284
blood vessel1.65e-2060
epithelial tube open at both ends1.65e-2060
blood vasculature1.65e-2060
vascular cord1.65e-2060
epithelial tube5.58e-20118
unilaminar epithelium8.94e-17138
artery3.20e-1542
arterial blood vessel3.20e-1542
arterial system3.20e-1542
systemic artery2.30e-1333
systemic arterial system2.30e-1333
muscle tissue2.83e-1163
musculature2.83e-1163
musculature of body2.83e-1163
skeletal muscle tissue6.86e-1161
striated muscle tissue6.86e-1161
myotome6.86e-1161
endothelium9.65e-1118
blood vessel endothelium9.65e-1118
cardiovascular system endothelium9.65e-1118
multilaminar epithelium1.27e-1082
dermomyotome4.71e-1070
trunk mesenchyme6.03e-10143
aorta7.80e-1021
aortic system7.80e-1021
somite1.54e-0983
paraxial mesoderm1.54e-0983
presomitic mesoderm1.54e-0983
presumptive segmental plate1.54e-0983
trunk paraxial mesoderm1.54e-0983
presumptive paraxial mesoderm1.54e-0983
mesoderm2.80e-09448
mesoderm-derived structure2.80e-09448
presumptive mesoderm2.80e-09448
trunk3.05e-09216
anatomical conduit4.55e-09241
simple squamous epithelium1.82e-0822
primary circulatory organ2.00e-0827
anatomical cluster3.41e-08286
squamous epithelium4.82e-0825
cell layer1.48e-07312
epithelium2.49e-07309
heart2.89e-0724
primitive heart tube2.89e-0724
primary heart field2.89e-0724
anterior lateral plate mesoderm2.89e-0724
heart tube2.89e-0724
heart primordium2.89e-0724
cardiac mesoderm2.89e-0724
cardiogenic plate2.89e-0724
heart rudiment2.89e-0724
anatomical system6.21e-07625
anatomical group9.45e-07626


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
CTCF#1066435.360256373075030.0064925092527670.0280530873298471
E2F1#186934.907389214879320.008460985347239390.0326699515187938
E2F6#187635.017155731697390.00791769806886330.0323469124007985
EGR1#195834.988179094810140.008056488137383440.0321689694364654
ELF1#199734.258097958807540.01295179875054610.0463911417006751
EP300#203336.77394172622320.003216880500103790.0167975492500545
FOS#235338.99795530889440.001372499272417130.0090005306738649
FOSL2#2355316.93020060456170.0002060162053171620.00243643148761398
FOXA1#3169311.08141974938550.000734755275698670.00582842976140767
FOXA2#3170324.63046375266526.68983856509345e-050.00107489238446122
GATA2#2624312.7449317335540.0004829527704283790.00437991528228287
GTF2F1#2962312.73966087675770.0004835525047438590.00435097269259446
HDAC2#3066313.41562023662630.0004140761399857210.00392571695569796
HNF4A#3172323.13229036295378.07584663437677e-050.00123164916274485
HNF4G#3174328.75342252644684.20470658818262e-050.000758961893126866
JUN#3725312.51282919233630.0005103313992726250.00445416187603491
JUND#372736.994663941871030.002921845042734990.0157247539120993
MAX#414936.452555509007120.003721913834265510.0187106117418462
MXI1#460139.96157162875930.001011470541259020.00721909190586694
MYC#460935.22228187160940.007020843755740150.0295438938315704
NR3C1#2908314.9730233311730.0002978331194675480.00309629635318249
PBX3#5090321.91451268674419.49854535978121e-050.00137113832595742
RAD21#5885310.35503389545630.0009004912073565420.0066652304185053
RXRA#6256320.07461713913330.0001235730348432220.00165671940770107
SIN3A#2594235.408884726815140.006318961977991520.0277649909554233
SMARCB1#6598318.25271578115740.000164397760679890.00203527000090648
SMARCC1#6599343.66335931963151.20046018043203e-050.000302180912952858
SMC3#9126315.04493284493280.0002935825420371870.00310056295963411
SP1#666735.69838137814090.005403962701712170.0247341774302795
TCF12#6938310.63446490218640.0008313523990202070.00630541853313518
TCF7L2#6934310.77017656313730.0008003181298398380.00615995468806418
TFAP2A#7020316.5186343730450.0002218033880766340.00248978117447717
TFAP2C#7022310.80922860986020.0007916746575753130.00617626873552761



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.

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