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Coexpression cluster:C2570

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Full id: C2570_mesenchymal_leiomyoma_Fibroblast_CD14_Mesothelial_Gingival_meningioma



Phase1 CAGE Peaks

Hg19::chr1:223900193..223900249,+p1@CAPN2
Hg19::chr1:223900250..223900274,+p3@CAPN2
Hg19::chr1:223900286..223900299,+p4@CAPN2
Hg19::chr1:223900302..223900328,+p2@CAPN2


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
mesoderm2.18e-19448
mesoderm-derived structure2.18e-19448
presumptive mesoderm2.18e-19448
somite1.02e-1783
paraxial mesoderm1.02e-1783
presomitic mesoderm1.02e-1783
presumptive segmental plate1.02e-1783
trunk paraxial mesoderm1.02e-1783
presumptive paraxial mesoderm1.02e-1783
multilaminar epithelium6.49e-1682
artery1.25e-1542
arterial blood vessel1.25e-1542
arterial system1.25e-1542
vasculature3.49e-1579
vascular system3.49e-1579
dermomyotome4.41e-1570
blood vessel7.56e-1560
epithelial tube open at both ends7.56e-1560
blood vasculature7.56e-1560
vascular cord7.56e-1560
musculoskeletal system9.48e-15167
vessel1.71e-1369
splanchnic layer of lateral plate mesoderm1.89e-1384
anatomical group2.65e-13626
anatomical system3.25e-13625
lateral plate mesoderm8.88e-13216
skeletal muscle tissue5.26e-1261
striated muscle tissue5.26e-1261
myotome5.26e-1261
systemic artery7.21e-1233
systemic arterial system7.21e-1233
trunk mesenchyme1.01e-11143
multi-cellular organism1.59e-11659
muscle tissue2.60e-1163
musculature2.60e-1163
musculature of body2.60e-1163
cardiovascular system1.47e-10110
unilaminar epithelium1.55e-10138
circulatory system4.43e-10113
germ layer5.33e-10604
embryonic tissue5.33e-10604
presumptive structure5.33e-10604
epiblast (generic)5.33e-10604
embryonic structure6.66e-10605
developing anatomical structure6.66e-10605
trunk7.85e-10216
surface structure8.02e-1095
epithelial tube1.97e-09118
embryo2.12e-08612
aorta9.86e-0821
aortic system9.86e-0821
mesenchyme5.48e-07238
entire embryonic mesenchyme5.48e-07238


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#90546.336201576962630.0006203100587215640.00512495548001119
CTCF#1066445.360256373075030.001211145381643620.00817758032799834
E2F1#186944.907389214879320.001724022357361790.0106547825895324
ELF1#199744.258097958807540.003041525565781240.0160984131646375
FOS#235348.99795530889440.0001525147711168630.0019501089839219
FOSL2#2355416.93020060456171.2165416097647e-050.00030410337286313
GATA1#2623413.56030814380042.95627390049268e-050.0006140618335194
HEY1#2346244.040111043105710.00375304636917980.0186197524939798
HMGN3#932448.178547723350590.0002234570284440470.002482198318833
JUN#3725412.51282919233634.07770316866756e-050.000743749984688214
JUND#372746.994663941871030.000417684217818580.00391936406332028
RAD21#5885410.35503389545638.6948481184721e-050.00129485418885656
SIN3A#2594245.408884726815140.001168172384885160.00796830747208026
SMC3#9126415.04493284493281.95092670935632e-050.000438272391048537
TAF1#687243.343046285745290.008005664898701650.0322458882469629
TBP#690843.706770687096390.005296377814784350.0244453068144892
YY1#752844.911170749853860.00171871838055440.0106915974118007
ZNF263#1012748.221841637010680.0002187871180958320.00249099616557403



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.