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Coexpression cluster:C3191: Difference between revisions

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{{Coexpression_clusters
{{Coexpression_clusters
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|full_id=C3191_bile_Smooth_leiomyoma_Hair_prostate_Preadipocyte_Myoblast
|full_id=C3191_bile_Smooth_leiomyoma_Hair_prostate_Preadipocyte_Myoblast
|id=C3191
|id=C3191

Revision as of 16:04, 12 September 2012


Full id: C3191_bile_Smooth_leiomyoma_Hair_prostate_Preadipocyte_Myoblast



Phase1 CAGE Peaks

Hg19::chr11:65686732..65686756,+p2@DRAP1
Hg19::chr11:65686776..65686787,+p9@DRAP1
Hg19::chr11:65686802..65686818,+p6@DRAP1


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
somite1.20e-2183
paraxial mesoderm1.20e-2183
presomitic mesoderm1.20e-2183
presumptive segmental plate1.20e-2183
trunk paraxial mesoderm1.20e-2183
presumptive paraxial mesoderm1.20e-2183
multilaminar epithelium2.07e-2082
trunk mesenchyme2.83e-18143
dermomyotome2.86e-1870
artery1.25e-1642
arterial blood vessel1.25e-1642
arterial system1.25e-1642
vessel2.33e-1569
blood vessel1.26e-1460
epithelial tube open at both ends1.26e-1460
blood vasculature1.26e-1460
vascular cord1.26e-1460
skeletal muscle tissue1.90e-1461
striated muscle tissue1.90e-1461
myotome1.90e-1461
vasculature2.84e-1479
vascular system2.84e-1479
systemic artery7.95e-1433
systemic arterial system7.95e-1433
surface structure2.15e-1395
trunk3.66e-13216
muscle tissue6.56e-1363
musculature6.56e-1363
musculature of body6.56e-1363
unilaminar epithelium1.08e-12138
epithelial tube1.18e-11118
splanchnic layer of lateral plate mesoderm2.01e-1184
integument1.89e-0945
integumental system1.89e-0945
mesenchyme1.91e-09238
entire embryonic mesenchyme1.91e-09238
organism subdivision2.06e-09365
mesoderm3.09e-09448
mesoderm-derived structure3.09e-09448
presumptive mesoderm3.09e-09448
musculoskeletal system1.85e-08167
cell layer2.28e-08312
epithelium2.77e-08309
skin of body3.40e-0840
cardiovascular system3.51e-08110
anatomical system1.19e-07625
anatomical group1.33e-07626
circulatory system1.49e-07113
aorta4.01e-0721
aortic system4.01e-0721


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
BCL11A#53335328.36945510360714.37778126761649e-050.000776645316474602
BCL3#602334.54710280373832.42397750207122e-050.000526425007982567
BCLAF1#9774321.65264761012189.8473954032885e-050.00138867422160957
CCNT2#90536.336201576962630.003930750035764890.0189251153874815
CTCF#1066435.360256373075030.0064925092527670.0278457218943671
E2F1#186934.907389214879320.008460985347239390.0323814301982606
E2F4#1874312.66806031528440.0004917987006298980.00435759434080648
E2F6#187635.017155731697390.00791769806886330.0320646969100785
EBF1#187938.9064668465690.00141523283560980.00912661328300416
EGR1#195834.988179094810140.008056488137383440.0319224358669167
ELF1#199734.258097958807540.01295179875054610.0460280696103268
EP300#203336.77394172622320.003216880500103790.0166940513068492
ETS1#211339.728760922202340.001085840092584840.00760182688225417
FOSL1#8061339.7135797163731.59554825631833e-050.000370223204491514
FOSL2#2355316.93020060456170.0002060162053171620.00242407914230724
FOXA1#3169311.08141974938550.000734755275698670.00579672958443068
GABPB1#255337.067683836182170.002832212825417420.0153666930891875
GATA3#2625327.2365163572064.94721007899563e-050.000848967586986895
HDAC2#3066313.41562023662630.0004140761399857210.00389987356695542
HMGN3#932438.178547723350590.001827766942164210.0108367954398347
HNF4A#3172323.13229036295378.07584663437677e-050.00122520823162068
HNF4G#3174328.75342252644684.20470658818262e-050.00075517687250766
IRF1#365937.63716375356390.002244692747297240.0127666212402645
JUND#372736.994663941871030.002921845042734990.0156217146727859
MEF2A#4205318.74323090964410.0001518243905622470.00194867734127202
MEF2C#4208341.31135449262411.41744912101957e-050.000340002224965923
MXI1#460139.96157162875930.001011470541259020.00718423366829101
MYC#460935.22228187160940.007020843755740150.0293311692870013
NFKB1#479035.488063424193840.006049381815655430.0268675903655215
NR2C2#7182332.61461090524092.88098172333076e-050.000603947912892295
NR3C1#2908314.9730233311730.0002978331194675480.0030797418974328
PAX5#507936.669565531177830.003370290999677260.0172383477014199
PBX3#5090321.91451268674419.49854535978121e-050.00136135388888458
POU2F2#545239.106124057742520.001324165192682130.00879847872239019
RAD21#5885310.35503389545630.0009004912073565420.00662065478388665
RXRA#6256320.07461713913330.0001235730348432220.00164867708047922
SIN3A#2594235.408884726815140.006318961977991520.0275551594997685
SMC3#9126315.04493284493280.0002935825420371870.0030812448103529
SP1#666735.69838137814090.005403962701712170.0245544685927395
SP2#6668326.15353049384465.58768218891694e-050.000937766254424387
SRF#6722313.79717826216780.0003806615025800190.00374032427019989
STAT1#6772320.70658749719920.0001125992441046670.00154509952109411
STAT2#6773365.26377118644073.59360517547754e-060.000118171451801542
TAF7#6879311.43306940492390.0006690181981945830.00540843653543185
TCF12#6938310.63446490218640.0008313523990202070.0062794252694924
TCF7L2#6934310.77017656313730.0008003181298398380.00611981440638035
USF1#739136.361499277207960.00388404057290560.0189598183404388
YY1#752834.911170749853860.008441455341808260.032810463507373
ZEB1#6935316.88843201754390.0002075486917327580.00242056703694891
ZNF143#7702313.50087655222790.0004062804962997170.00387892209096317



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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