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Coexpression cluster:C3167: Difference between revisions

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{{Coexpression_clusters
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|full_id=C3167_Alveolar_embryonic_Smooth_Mesenchymal_Pericytes_Hepatic_Endothelial
|id=C3167
}}

Latest revision as of 12:20, 17 September 2013


Full id: C3167_Alveolar_embryonic_Smooth_Mesenchymal_Pericytes_Hepatic_Endothelial



Phase1 CAGE Peaks

Hg19::chr11:60609519..60609536,+p3@CCDC86
Hg19::chr11:60609537..60609567,+p2@CCDC86
Hg19::chr11:60609568..60609594,+p1@CCDC86


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>disease_data<br>

Cell Type
Ontology termp-valuen
embryonic cell1.33e-26250
animal cell1.57e-23679
eukaryotic cell1.57e-23679
epithelial cell1.21e-22253
mesodermal cell1.21e-19121
contractile cell3.97e-1359
native cell4.56e-13722
non-terminally differentiated cell2.11e-12106
muscle precursor cell1.35e-1158
myoblast1.35e-1158
multi-potent skeletal muscle stem cell1.35e-1158
muscle cell2.57e-1155
electrically responsive cell4.30e-1161
electrically active cell4.30e-1161
smooth muscle cell9.64e-1043
smooth muscle myoblast9.64e-1043
squamous epithelial cell2.48e-0963
somatic cell4.98e-09588
endothelial cell2.25e-0836
meso-epithelial cell2.78e-0845
vascular associated smooth muscle cell4.08e-0832
lining cell4.75e-0858
barrier cell4.75e-0858
blood vessel endothelial cell1.16e-0718
embryonic blood vessel endothelial progenitor cell1.16e-0718
epithelial cell of nephron1.55e-0715
endothelial cell of vascular tree7.67e-0724
Uber Anatomy
Ontology termp-valuen
unilaminar epithelium1.22e-17148
epithelial vesicle3.07e-1778
trunk9.87e-15199
mesenchyme1.23e-14160
entire embryonic mesenchyme1.23e-14160
multilaminar epithelium3.07e-1483
somite4.31e-1471
presomitic mesoderm4.31e-1471
presumptive segmental plate4.31e-1471
dermomyotome4.31e-1471
trunk paraxial mesoderm4.31e-1471
paraxial mesoderm1.50e-1372
presumptive paraxial mesoderm1.50e-1372
dense mesenchyme tissue3.87e-1373
cell layer4.41e-13309
trunk mesenchyme5.08e-13122
vasculature5.39e-1378
vascular system5.39e-1378
epithelial tube1.13e-12117
epithelium3.57e-12306
organism subdivision1.05e-11264
vessel2.16e-1168
skeletal muscle tissue2.34e-1162
striated muscle tissue2.34e-1162
myotome2.34e-1162
epithelial tube open at both ends5.05e-1159
blood vessel5.05e-1159
blood vasculature5.05e-1159
vascular cord5.05e-1159
muscle tissue2.37e-1064
musculature2.37e-1064
musculature of body2.37e-1064
artery3.43e-1042
arterial blood vessel3.43e-1042
arterial system3.43e-1042
splanchnic layer of lateral plate mesoderm6.05e-0983
simple squamous epithelium7.13e-0822
blood vessel endothelium1.16e-0718
endothelium1.16e-0718
cardiovascular system endothelium1.16e-0718
nephron epithelium1.55e-0715
renal tubule1.55e-0715
nephron tubule1.55e-0715
nephron1.55e-0715
uriniferous tubule1.55e-0715
nephrogenic mesenchyme1.55e-0715
multi-tissue structure3.20e-07342
parenchyma4.13e-0715
squamous epithelium6.79e-0725
Disease
Ontology termp-valuen
disease of cellular proliferation9.40e-15239
cancer7.22e-14235
cell type cancer1.05e-08143
carcinoma2.47e-07106


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)
MA0003.10.401049
MA0004.11.93041
MA0006.10.639288
MA0007.10.804807
MA0009.11.3275
MA0014.10.758317
MA0017.10.686276
MA0019.10.990656
MA0024.11.21731
MA0025.11.46617
MA0027.12.95767
MA0028.10.658629
MA0029.11.23771
MA0030.11.22561
MA0031.11.15713
MA0038.10.94098
MA0040.11.24388
MA0041.10.847069
MA0042.10.810843
MA0043.11.32783
MA0046.11.31611
MA0048.10.341392
MA0050.11.90116
MA0051.15.06231
MA0052.11.24796
MA0055.10.190716
MA0056.10
MA0057.11.59304
MA0058.10.716037
MA0059.10.714521
MA0060.10.492218
MA0061.10.456531
MA0063.10
MA0066.10.941452
MA0067.11.65513
MA0068.10.405474
MA0069.11.31207
MA0070.12.89432
MA0071.10.897953
MA0072.11.29561
MA0073.11.36698
MA0074.10.935474
MA0076.10.734647
MA0077.11.28751
MA0078.11.04495
MA0081.10.714712
MA0083.11.33535
MA0084.11.84562
MA0087.11.29304
MA0088.10.257905
MA0089.10
MA0090.10.751469
MA0091.10.829044
MA0092.10.785956
MA0093.10.642957
MA0095.10
MA0098.10
MA0100.10.956299
MA0101.10.646932
MA0103.10.628063
MA0105.10.31555
MA0106.10.986396
MA0107.10.556367
MA0108.21.15387
MA0109.10
MA0111.10.767139
MA0113.11.00436
MA0114.10.549955
MA0115.11.57693
MA0116.10.560723
MA0117.11.36676
MA0119.10.695578
MA0122.11.39371
MA0124.11.53432
MA0125.11.44766
MA0130.10
MA0131.11.06461
MA0132.10
MA0133.10
MA0135.11.35921
MA0136.10.948776
MA0139.10.440097
MA0140.10.894983
MA0141.10.712476
MA0142.11.12317
MA0143.11.00455
MA0144.11.31729
MA0145.10.752137
MA0146.10.107247
MA0147.11.38767
MA0148.10.854239
MA0149.10.884158
MA0062.20.449458
MA0035.20.894194
MA0039.20.195278
MA0138.21.04628
MA0002.20.476938
MA0137.20.666381
MA0104.21.2307
MA0047.20.973066
MA0112.20.264678
MA0065.20.277623
MA0150.10.744617
MA0151.10
MA0152.10.902317
MA0153.11.43021
MA0154.10.312019
MA0155.10.256269
MA0156.10.669101
MA0157.11.09377
MA0158.10
MA0159.10.565904
MA0160.10.871361
MA0161.10
MA0162.10.149099
MA0163.10.122425
MA0164.11.01792
MA0080.20.643061
MA0018.23.70709
MA0099.20.902716
MA0079.20.0107199
MA0102.21.88331
MA0258.10.519674
MA0259.12.40872
MA0442.10



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-050.00129274577711209
BHLHE40#8553344.87181354697741.10603738662898e-050.000283747085782717
BRCA1#672320.18423064322380.0001215704860271640.00163934150938553
CCNT2#90536.336201576962630.003930750035764890.0189224984090919
CEBPB#105137.971147625824820.001974187055288560.0114954349836798
CHD2#1106310.34402283411690.0009033701102746880.00658572322678893
E2F4#1874312.66806031528440.0004917987006298980.00435648553817523
E2F6#187635.017155731697390.00791769806886330.0320559958371071
EGR1#195834.988179094810140.008056488137383440.0319188029505781
ELF1#199734.258097958807540.01295179875054610.046018674209304
EP300#203336.77394172622320.003216880500103790.0166915631235264
ETS1#211339.728760922202340.001085840092584840.00760080787060776
FOSL2#2355316.93020060456170.0002060162053171620.00242326010441706
FOXA1#3169311.08141974938550.000734755275698670.00579541622526194
GABPB1#255337.067683836182170.002832212825417420.0153650966325786
HDAC2#3066313.41562023662630.0004140761399857210.0038988187868706
HMGN3#932438.178547723350590.001827766942164210.0108349501460261
IRF1#365937.63716375356390.002244692747297240.0127645358725349
IRF4#3662321.91451268674419.49854535978121e-050.00136098035235312
JUND#372736.994663941871030.002921845042734990.0156193158836157
MAFF#23764356.31535648994525.59409009993116e-060.000168758283057975
MAX#414936.452555509007120.003721913834265510.018581813611399
MEF2A#4205318.74323090964410.0001518243905622470.00194819849194378
MXI1#460139.96157162875930.001011470541259020.00718325662032851
MYC#460935.22228187160940.007020843755740150.0293253039915912
NFKB1#479035.488063424193840.006049381815655430.026865305415029
NR3C1#2908314.9730233311730.0002978331194675480.00307943700268006
NRF1#4899312.21027944771090.0005492172401020010.00469622558858792
PAX5#507936.669565531177830.003370290999677260.0172366594052835
PBX3#5090321.91451268674419.49854535978121e-050.00136116709499203
POU2F2#545239.106124057742520.001324165192682130.00879735932306164
REST#597839.650028716128020.001112636247114590.00765397292928472
RFX5#5993312.04791082719510.0005717246050312580.00483132502830808
SETDB1#9869340.32002617801051.52461559299059e-050.000358140638588269
SIN3A#2594235.408884726815140.006318961977991520.0275505581539391
SIX5#147912317.0867153554590.0002004060546325010.00239038464364593
SP1#666735.69838137814090.005403962701712170.0245512641640907
SRF#6722313.79717826216780.0003806615025800190.00373962060652381
TCF12#6938310.63446490218640.0008313523990202070.0062780631381975
THAP1#55145331.36914460285133.23800758564397e-050.000645124521627376
USF1#739136.361499277207960.00388404057290560.0189580461463611
USF2#7392312.99219738506960.0004558979393427810.00420502736792553
YY1#752834.911170749853860.008441455341808260.0328068006714216
ZBTB7A#5134137.35190930787590.002516255860282270.01396435760625
ZEB1#6935316.88843201754390.0002075486917327580.0024200265508404



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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