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Coexpression cluster:C2131: Difference between revisions

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{{Coexpression_clusters
{{Coexpression_clusters
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|full_id=C2131_Smooth_Fibroblast_gall_leiomyoma_bone_Chondrocyte_mesenchymal
|full_id=C2131_Smooth_Fibroblast_gall_leiomyoma_bone_Chondrocyte_mesenchymal
|id=C2131
|id=C2131

Revision as of 14:49, 12 September 2012


Full id: C2131_Smooth_Fibroblast_gall_leiomyoma_bone_Chondrocyte_mesenchymal



Phase1 CAGE Peaks

Hg19::chr11:44117206..44117218,+p2@EXT2
Hg19::chr11:44117219..44117240,+p1@EXT2
Hg19::chr11:44117242..44117253,+p3@EXT2
Hg19::chr11:44117260..44117283,+p4@EXT2


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
vasculature1.75e-1779
vascular system1.75e-1779
trunk mesenchyme3.51e-17143
multilaminar epithelium1.26e-1682
vessel2.04e-1669
trunk3.75e-16216
organism subdivision4.36e-16365
somite7.18e-1683
paraxial mesoderm7.18e-1683
presomitic mesoderm7.18e-1683
presumptive segmental plate7.18e-1683
trunk paraxial mesoderm7.18e-1683
presumptive paraxial mesoderm7.18e-1683
epithelial tube1.18e-15118
splanchnic layer of lateral plate mesoderm1.60e-1584
blood vessel3.28e-1560
epithelial tube open at both ends3.28e-1560
blood vasculature3.28e-1560
vascular cord3.28e-1560
artery1.02e-1442
arterial blood vessel1.02e-1442
arterial system1.02e-1442
unilaminar epithelium7.30e-14138
dermomyotome9.64e-1470
multi-cellular organism1.10e-13659
skeletal muscle tissue1.65e-1361
striated muscle tissue1.65e-1361
myotome1.65e-1361
muscle tissue2.27e-1363
musculature2.27e-1363
musculature of body2.27e-1363
anatomical system4.26e-13625
systemic artery4.72e-1333
systemic arterial system4.72e-1333
anatomical group9.02e-13626
mesenchyme3.11e-12238
entire embryonic mesenchyme3.11e-12238
cell layer4.63e-12312
epithelium6.43e-12309
multi-tissue structure2.65e-11347
surface structure9.15e-1195
cardiovascular system1.49e-09110
circulatory system2.30e-09113
anatomical cluster2.43e-08286
anatomical conduit3.54e-08241
embryonic structure3.73e-07605
developing anatomical structure3.73e-07605
integument3.75e-0745
integumental system3.75e-0745
germ layer5.47e-07604
embryonic tissue5.47e-07604
presumptive structure5.47e-07604
epiblast (generic)5.47e-07604
skin of body6.80e-0740
embryo6.91e-07612
aorta8.55e-0721
aortic system8.55e-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
CCNT2#90546.336201576962630.0006203100587215640.00511241810470498
CTCF#1066445.360256373075030.001211145381643620.00815701376884493
CTCFL#140690419.74647435897446.5732084880439e-060.000192620460517064
ELF1#199744.258097958807540.003041525565781240.0160536659708206
ETS1#211349.728760922202340.0001115955317418140.00154308562684804
FOXA1#3169411.08141974938556.62943068949433e-050.00106913389712801
HEY1#2346244.040111043105710.00375304636917980.0185527717967894
HMGN3#932448.178547723350590.0002234570284440470.00247745526472058
NRF1#4899412.21027944771094.49717228915276e-050.000791773730119395
SIN3A#2594245.408884726815140.001168172384885160.00794185364568551
SMC3#9126415.04493284493281.95092670935632e-050.000437144034753196
SP2#6668426.15353049384462.13562021071447e-067.73914084617658e-05
TAF1#687243.343046285745290.008005664898701650.0321244721387598
TBP#690843.706770687096390.005296377814784350.0243484638875897
ZNF143#7702413.50087655222793.00867915035614e-050.000619525713296618



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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