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Coexpression cluster:C1911: Difference between revisions

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{{Coexpression_clusters
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|full_id=C1911_Smooth_mesenchymal_Fibroblast_leiomyoma_Preadipocyte_Adipocyte_osteoclastoma
|id=C1911
}}

Latest revision as of 11:54, 17 September 2013


Full id: C1911_Smooth_mesenchymal_Fibroblast_leiomyoma_Preadipocyte_Adipocyte_osteoclastoma



Phase1 CAGE Peaks

Hg19::chr2:55277453..55277464,-p7@RTN4
Hg19::chr2:55277485..55277498,-p5@RTN4
Hg19::chr2:55277522..55277533,-p6@RTN4
Hg19::chr2:55277578..55277596,-p1@RTN4
Hg19::chr2:55277626..55277648,-p3@RTN4


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
anatomical system6.05e-19624
multi-cellular organism1.04e-18656
anatomical group1.68e-18625
multilaminar epithelium1.20e-1783
vasculature3.38e-1778
vascular system3.38e-1778
epithelial vesicle3.52e-1678
dense mesenchyme tissue5.41e-1673
somite5.98e-1671
presomitic mesoderm5.98e-1671
presumptive segmental plate5.98e-1671
dermomyotome5.98e-1671
trunk paraxial mesoderm5.98e-1671
paraxial mesoderm7.00e-1672
presumptive paraxial mesoderm7.00e-1672
vessel4.69e-1568
artery8.48e-1542
arterial blood vessel8.48e-1542
arterial system8.48e-1542
epithelial tube open at both ends1.53e-1459
blood vessel1.53e-1459
blood vasculature1.53e-1459
vascular cord1.53e-1459
cell layer1.80e-14309
splanchnic layer of lateral plate mesoderm2.99e-1483
mesoderm3.89e-14315
mesoderm-derived structure3.89e-14315
presumptive mesoderm3.89e-14315
skeletal muscle tissue4.21e-1462
striated muscle tissue4.21e-1462
myotome4.21e-1462
epithelium8.38e-14306
muscle tissue3.15e-1364
musculature3.15e-1364
musculature of body3.15e-1364
systemic artery5.04e-1333
systemic arterial system5.04e-1333
musculoskeletal system6.27e-13167
unilaminar epithelium2.02e-12148
cardiovascular system7.91e-12109
epithelial tube1.34e-11117
embryonic structure1.57e-11564
developing anatomical structure2.01e-11581
embryo2.27e-11592
germ layer3.29e-11560
germ layer / neural crest3.29e-11560
embryonic tissue3.29e-11560
presumptive structure3.29e-11560
germ layer / neural crest derived structure3.29e-11560
epiblast (generic)3.29e-11560
circulatory system5.35e-11112
organism subdivision8.07e-11264
anatomical conduit1.31e-10240
trunk mesenchyme1.32e-10122
surface structure5.94e-1099
mesenchyme3.59e-09160
entire embryonic mesenchyme3.59e-09160
trunk1.43e-08199
tube1.17e-07192
aorta1.34e-0721
aortic system1.34e-0721
lateral plate mesoderm3.03e-07203
anatomical cluster5.48e-07373
multi-tissue structure5.93e-07342


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)
MA0003.10.481059
MA0004.10.626788
MA0006.10.452993
MA0007.10.606704
MA0009.11.11255
MA0014.10.0418333
MA0017.10.496101
MA0019.10.784036
MA0024.11.00439
MA0025.11.24931
MA0027.12.73598
MA0028.10.470679
MA0029.11.02437
MA0030.11.01252
MA0031.10.945567
MA0038.10.736268
MA0040.11.03042
MA0041.10.64667
MA0042.10.612397
MA0043.11.11288
MA0046.11.10134
MA0048.11.08193
MA0050.10.613347
MA0051.10.731787
MA0052.11.03442
MA0055.16.52915
MA0056.10
MA0057.10.554727
MA0058.10.523638
MA0059.10.522232
MA0060.12.35759
MA0061.10.291022
MA0063.10
MA0066.10.736721
MA0067.11.43651
MA0068.10.247962
MA0069.11.09737
MA0070.11.08584
MA0071.10.695094
MA0072.11.0812
MA0073.16.69924
MA0074.10.730989
MA0076.10.540943
MA0077.12.43492
MA0078.10.836493
MA0081.10.522409
MA0083.11.12028
MA0084.11.62584
MA0087.11.07867
MA0088.10.132006
MA0089.10
MA0090.10.556637
MA0091.10.629594
MA0092.10.588959
MA0093.10.456342
MA0095.10
MA0098.10
MA0100.12.96921
MA0101.10.459973
MA0103.10.442769
MA0105.10.175503
MA0106.10.779931
MA0107.10.378225
MA0108.20.94238
MA0109.10
MA0111.10.5713
MA0113.10.797251
MA0114.10.372523
MA0115.11.35895
MA0116.10.382106
MA0117.11.1512
MA0119.10.504689
MA0122.11.17777
MA0124.11.31673
MA0125.11.23103
MA0130.10
MA0131.10.855546
MA0132.10
MA0133.10
MA0135.11.14377
MA0136.10.743749
MA0139.10.759606
MA0140.11.65391
MA0141.10.520334
MA0142.10.912455
MA0143.10.797437
MA0144.10.356507
MA0145.10.442008
MA0146.10.0359558
MA0147.11.00307
MA0148.10.653474
MA0149.10.681935
MA0062.20.284987
MA0035.20.691506
MA0039.20.801354
MA0138.20.837782
MA0002.20.30855
MA0137.20.47779
MA0104.20.320919
MA0047.20.767096
MA0112.20.136971
MA0065.20.146576
MA0150.10.550239
MA0151.10
MA0152.10.69926
MA0153.11.21379
MA0154.15.57055
MA0155.10.130813
MA0156.10.480289
MA0157.10.883854
MA0158.10
MA0159.10.386729
MA0160.10.669748
MA0161.10
MA0162.10.81299
MA0163.10.382496
MA0164.10.810347
MA0080.20.456437
MA0018.20.781393
MA0099.22.8068
MA0079.21.81596
MA0102.21.66336
MA0258.10.345771
MA0259.10.395396
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
BCLAF1#9774521.65264761012182.09874458450681e-071.12003467379309e-05
CCNT2#90556.336201576962639.78880505817628e-050.0013913078544786
CEBPB#105157.971147625824823.10621793420244e-050.000628823986877628
CHD2#1106510.34402283411698.43981772346334e-060.000230323000580295
CTCF#1066455.360256373075030.0002259278299937090.00250033661510151
E2F1#186954.907389214879320.0003512818099256460.00353274154519254
E2F4#1874512.66806031528443.06319883889696e-060.000103533146775262
E2F6#187655.017155731697390.0003144978599297790.00323063263432735
EBF1#187958.9064668465691.78355672307702e-050.000406443117175302
ELF1#199754.258097958807540.0007142416939776840.00573540583402548
FOS#235358.99795530889441.69470025615156e-050.000389508802931806
FOSL1#8061539.7135797163731.01017090471068e-087.650561212261e-07
FOSL2#2355516.93020060456177.18315284751475e-073.21010398049462e-05
GABPB1#255357.067683836182175.6685482528729e-050.00094905019394324
GTF2B#2959531.94382993432423.00149609204784e-082.03818758359808e-06
HDAC2#3066513.41562023662632.29961139448262e-068.18293405207396e-05
HEY1#2346254.040111043105710.0009288852205177990.00674724186574339
HMGN3#932458.178547723350592.73180911341838e-050.000582497778677627
IRF1#365957.63716375356393.84754333311872e-050.000724808041427826
IRF3#3661546.98195221148964.35776524686345e-093.54455330698732e-07
JUN#3725512.51282919233633.25800591331781e-060.000109198613472721
JUNB#3726530.61063265982113.71486060097063e-082.46647378451857e-06
JUND#372756.994663941871035.97069468343598e-050.000984952427805038
MXI1#460159.96157162875931.01894348670516e-050.000266710372952381
MYC#460955.22228187160940.0002573944848850610.00276677877798589
NFKB1#479055.488063424193840.0002008162847462320.00239227238081575
NFYA#4800518.42558069983054.70418681889082e-072.22408586318759e-05
NFYB#4801516.75979325353657.55590255814554e-073.32685879962126e-05
NR3C1#2908514.9730233311731.32777388277837e-065.25270365695038e-05
PAX5#507956.669565531177837.57493746384605e-050.00117081381350691
PBX3#5090521.91451268674411.97628413609567e-071.07165700358097e-05
POU2F2#545259.106124057742521.59639992500654e-050.000369927694181847
RDBP#79365153.6384039900251.15853713054028e-111.44215088648983e-09
REST#597859.650028716128021.19441074361324e-050.000301603151963788
SIN3A#2594255.408884726815140.0002159522671657270.00248308255317862
SP1#666755.69838137814090.000166391843712550.00204420630108164
SP2#6668526.15353049384468.16125998835445e-084.87616608652031e-06
SPI1#668858.204323508522732.68916109982495e-050.000574929981790415
SREBF1#6720547.00584944048834.34669369311096e-093.54382781120075e-07
TAF1#687253.343046285745290.002394600090870310.0135476510774867
TAF7#6879511.43306940492395.11611886715123e-060.000157477848030182
TBP#690853.706770687096390.001428755106721120.00919734680663506
TCF12#6938510.63446490218647.34844389925727e-060.000211306203853119
TCF7L2#6934510.77017656313736.89693748574565e-060.0001999748067945
TFAP2A#7020516.5186343730458.12390055913032e-073.54111874163193e-05
TFAP2C#7022510.80922860986026.77323239348459e-060.000197429421697778
USF1#739156.361499277207969.59569864925045e-050.00137001390461937
YY1#752854.911170749853860.00034993140821360.00352867493892248
ZBTB7A#5134157.35190930787594.65425347594289e-050.000816264615909318
ZEB1#6935516.88843201754397.27243686732534e-073.2334015921098e-05
ZNF263#1012758.221841637010682.6606316672286e-050.000571874275969722



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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