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Coexpression cluster:C1911: Difference between revisions

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|ontology_enrichment_disease=
|ontology_enrichment_disease=
|ontology_enrichment_uberon=UBERON:0000914!7.48e-19!83;UBERON:0002329!7.48e-19!83;UBERON:0003077!7.48e-19!83;UBERON:0003059!7.48e-19!83;UBERON:0007282!7.48e-19!83;UBERON:0009618!7.48e-19!83;UBERON:0007285!7.48e-19!83;UBERON:0000468!1.95e-18!659;UBERON:0000467!3.84e-18!625;UBERON:0002049!5.14e-18!79;UBERON:0007798!5.14e-18!79;UBERON:0000480!1.05e-17!626;UBERON:0000486!1.36e-17!82;UBERON:0000055!8.16e-16!69;UBERON:0004290!9.57e-16!70;UBERON:0000475!2.12e-15!365;UBERON:0001981!3.82e-15!60;UBERON:0007500!3.82e-15!60;UBERON:0004537!3.82e-15!60;UBERON:0006965!3.82e-15!60;UBERON:0001637!7.70e-15!42;UBERON:0003509!7.70e-15!42;UBERON:0004572!7.70e-15!42;UBERON:0004872!1.30e-14!84;UBERON:0005256!2.34e-14!143;UBERON:0000119!5.64e-14!312;UBERON:0001134!1.74e-13!61;UBERON:0002036!1.74e-13!61;UBERON:0003082!1.74e-13!61;UBERON:0000483!2.52e-13!309;UBERON:0004573!4.35e-13!33;UBERON:0004571!4.35e-13!33;UBERON:0002385!9.33e-13!63;UBERON:0001015!9.33e-13!63;UBERON:0000383!9.33e-13!63;UBERON:0000923!1.38e-12!604;UBERON:0005291!1.38e-12!604;UBERON:0006598!1.38e-12!604;UBERON:0002532!1.38e-12!604;UBERON:0002050!2.13e-12!605;UBERON:0005423!2.13e-12!605;UBERON:0003914!3.77e-12!118;UBERON:0004535!5.35e-12!110;UBERON:0000922!1.47e-11!612;UBERON:0002100!1.65e-11!216;UBERON:0002204!1.71e-11!167;UBERON:0001009!3.94e-11!113;UBERON:0004111!1.61e-10!241;UBERON:0000490!1.91e-10!138;UBERON:0000477!5.24e-10!286;UBERON:0003102!5.50e-10!95;UBERON:0000926!2.52e-09!448;UBERON:0004120!2.52e-09!448;UBERON:0006603!2.52e-09!448;UBERON:0000947!5.73e-08!21;UBERON:0010191!5.73e-08!21;UBERON:0000025!1.06e-07!194;UBERON:0003081!2.34e-07!216;UBERON:0000481!7.44e-07!347;UBERON:0002199!7.74e-07!45;UBERON:0002416!7.74e-07!45
|ontology_enrichment_uberon=UBERON:0000914!7.48e-19!83;UBERON:0002329!7.48e-19!83;UBERON:0003077!7.48e-19!83;UBERON:0003059!7.48e-19!83;UBERON:0007282!7.48e-19!83;UBERON:0009618!7.48e-19!83;UBERON:0007285!7.48e-19!83;UBERON:0000468!1.95e-18!659;UBERON:0000467!3.84e-18!625;UBERON:0002049!5.14e-18!79;UBERON:0007798!5.14e-18!79;UBERON:0000480!1.05e-17!626;UBERON:0000486!1.36e-17!82;UBERON:0000055!8.16e-16!69;UBERON:0004290!9.57e-16!70;UBERON:0000475!2.12e-15!365;UBERON:0001981!3.82e-15!60;UBERON:0007500!3.82e-15!60;UBERON:0004537!3.82e-15!60;UBERON:0006965!3.82e-15!60;UBERON:0001637!7.70e-15!42;UBERON:0003509!7.70e-15!42;UBERON:0004572!7.70e-15!42;UBERON:0004872!1.30e-14!84;UBERON:0005256!2.34e-14!143;UBERON:0000119!5.64e-14!312;UBERON:0001134!1.74e-13!61;UBERON:0002036!1.74e-13!61;UBERON:0003082!1.74e-13!61;UBERON:0000483!2.52e-13!309;UBERON:0004573!4.35e-13!33;UBERON:0004571!4.35e-13!33;UBERON:0002385!9.33e-13!63;UBERON:0001015!9.33e-13!63;UBERON:0000383!9.33e-13!63;UBERON:0000923!1.38e-12!604;UBERON:0005291!1.38e-12!604;UBERON:0006598!1.38e-12!604;UBERON:0002532!1.38e-12!604;UBERON:0002050!2.13e-12!605;UBERON:0005423!2.13e-12!605;UBERON:0003914!3.77e-12!118;UBERON:0004535!5.35e-12!110;UBERON:0000922!1.47e-11!612;UBERON:0002100!1.65e-11!216;UBERON:0002204!1.71e-11!167;UBERON:0001009!3.94e-11!113;UBERON:0004111!1.61e-10!241;UBERON:0000490!1.91e-10!138;UBERON:0000477!5.24e-10!286;UBERON:0003102!5.50e-10!95;UBERON:0000926!2.52e-09!448;UBERON:0004120!2.52e-09!448;UBERON:0006603!2.52e-09!448;UBERON:0000947!5.73e-08!21;UBERON:0010191!5.73e-08!21;UBERON:0000025!1.06e-07!194;UBERON:0003081!2.34e-07!216;UBERON:0000481!7.44e-07!347;UBERON:0002199!7.74e-07!45;UBERON:0002416!7.74e-07!45
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}}
}}

Revision as of 12:44, 5 September 2012


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
somite7.48e-1983
paraxial mesoderm7.48e-1983
presomitic mesoderm7.48e-1983
presumptive segmental plate7.48e-1983
trunk paraxial mesoderm7.48e-1983
presumptive paraxial mesoderm7.48e-1983
multi-cellular organism1.95e-18659
anatomical system3.84e-18625
vasculature5.14e-1879
vascular system5.14e-1879
anatomical group1.05e-17626
multilaminar epithelium1.36e-1782
vessel8.16e-1669
dermomyotome9.57e-1670
organism subdivision2.12e-15365
blood vessel3.82e-1560
epithelial tube open at both ends3.82e-1560
blood vasculature3.82e-1560
vascular cord3.82e-1560
artery7.70e-1542
arterial blood vessel7.70e-1542
arterial system7.70e-1542
splanchnic layer of lateral plate mesoderm1.30e-1484
trunk mesenchyme2.34e-14143
cell layer5.64e-14312
skeletal muscle tissue1.74e-1361
striated muscle tissue1.74e-1361
myotome1.74e-1361
epithelium2.52e-13309
systemic artery4.35e-1333
systemic arterial system4.35e-1333
muscle tissue9.33e-1363
musculature9.33e-1363
musculature of body9.33e-1363
germ layer1.38e-12604
embryonic tissue1.38e-12604
presumptive structure1.38e-12604
epiblast (generic)1.38e-12604
embryonic structure2.13e-12605
developing anatomical structure2.13e-12605
epithelial tube3.77e-12118
cardiovascular system5.35e-12110
embryo1.47e-11612
trunk1.65e-11216
musculoskeletal system1.71e-11167
circulatory system3.94e-11113
anatomical conduit1.61e-10241
unilaminar epithelium1.91e-10138
anatomical cluster5.24e-10286
surface structure5.50e-1095
mesoderm2.52e-09448
mesoderm-derived structure2.52e-09448
presumptive mesoderm2.52e-09448
aorta5.73e-0821
aortic system5.73e-0821
tube1.06e-07194
lateral plate mesoderm2.34e-07216
multi-tissue structure7.44e-07347
integument7.74e-0745
integumental system7.74e-0745


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
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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