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{{Coexpression_clusters
{{Coexpression_clusters
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|full_id=C4749_Mesenchymal_Hepatic_sacrococcigeal_rhabdomyosarcoma_Smooth_Trabecular_Fibroblast
|full_id=C4749_Mesenchymal_Hepatic_sacrococcigeal_rhabdomyosarcoma_Smooth_Trabecular_Fibroblast
|id=C4749
|id=C4749

Revision as of 17:53, 12 September 2012


Full id: C4749_Mesenchymal_Hepatic_sacrococcigeal_rhabdomyosarcoma_Smooth_Trabecular_Fibroblast



Phase1 CAGE Peaks

Hg19::chr8:37654369..37654415,+p1@GPR124
Hg19::chr8:37654427..37654436,+p3@GPR124
Hg19::chr8:37654457..37654468,+p2@GPR124


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
multi-cellular organism3.59e-15659
somite4.21e-1383
paraxial mesoderm4.21e-1383
presomitic mesoderm4.21e-1383
presumptive segmental plate4.21e-1383
trunk paraxial mesoderm4.21e-1383
presumptive paraxial mesoderm4.21e-1383
splanchnic layer of lateral plate mesoderm3.90e-1284
dermomyotome4.38e-1270
vasculature6.99e-1279
vascular system6.99e-1279
muscle tissue2.03e-1163
musculature2.03e-1163
musculature of body2.03e-1163
organism subdivision6.44e-11365
skeletal muscle tissue8.15e-1161
striated muscle tissue8.15e-1161
myotome8.15e-1161
circulatory system1.41e-10113
cardiovascular system1.77e-10110
anatomical system7.96e-10625
anatomical group8.96e-10626
trunk mesenchyme1.09e-09143
multilaminar epithelium1.65e-0982
vessel2.09e-0969
blood vessel8.54e-0960
epithelial tube open at both ends8.54e-0960
blood vasculature8.54e-0960
vascular cord8.54e-0960
embryo1.05e-07612
embryonic structure2.75e-07605
developing anatomical structure2.75e-07605
epithelial tube4.10e-07118
germ layer5.19e-07604
embryonic tissue5.19e-07604
presumptive structure5.19e-07604
epiblast (generic)5.19e-07604
tissue5.45e-07787
multi-tissue structure9.58e-07347


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#90536.336201576962630.003930750035764890.0191279285707413
CTCF#1066435.360256373075030.0064925092527670.0281485812549186
E2F1#186934.907389214879320.008460985347239390.0327911848256024
E2F6#187635.017155731697390.00791769806886330.032452276936306
EGR1#195834.988179094810140.008056488137383440.0322664249944468
FOSL1#8061339.7135797163731.59554825631833e-050.000372790747967853
JUND#372736.994663941871030.002921845042734990.0157735229204073
TFAP2A#7020316.5186343730450.0002218033880766340.0024964892819631
TFAP2C#7022310.80922860986020.0007916746575753130.00619245877490324
ZBTB7A#5134137.35190930787590.002516255860282270.0141014834616881
ZNF143#7702313.50087655222790.0004062804962997170.00390570036386654



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.