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Coexpression cluster:C1962

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Full id: C1962_Adipocyte_Synoviocyte_Mast_mature_tenocyte_Chondrocyte_leiomyoblastoma



Phase1 CAGE Peaks

Hg19::chr5:54721817..54721840,-p@chr5:54721817..54721840
-
Hg19::chr5:54771166..54771206,+p@chr5:54771166..54771206
+
Hg19::chr5:54830488..54830506,-p2@RNF138P1
Hg19::chr5:54830511..54830588,-p1@RNF138P1
Hg19::chr5:54830784..54830799,-p1@PPAP2A


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


GO IDGO nameFDR corrected p-value
GO:0008195phosphatidate phosphatase activity0.0139516400949588
GO:0008354germ cell migration0.0139516400949588
GO:0046839phospholipid dephosphorylation0.028399509486818
GO:0019216regulation of lipid metabolic process0.028399509486818
GO:0030521androgen receptor signaling pathway0.028399509486818
GO:0007205protein kinase C activation0.028399509486818
GO:0030518steroid hormone receptor signaling pathway0.028399509486818
GO:0030258lipid modification0.028399509486818
GO:0030522intracellular receptor-mediated signaling pathway0.028399509486818
GO:0032147activation of protein kinase activity0.0325231595799832
GO:0007200G-protein signaling, coupled to IP3 second messenger (phospholipase C activating)0.0371594678851849
GO:0048015phosphoinositide-mediated signaling0.0454807681646362
GO:0045860positive regulation of protein kinase activity0.0454807681646362
GO:0033674positive regulation of kinase activity0.0454807681646362
GO:0051347positive regulation of transferase activity0.0454807681646362



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>


Cell Type
Ontology termp-valuen
fat cell2.59e-1215
fibroblast8.47e-1076
Uber Anatomy
Ontology termp-valuen
adult organism3.16e-27114
multi-tissue structure3.81e-12342
neural tube1.48e-1056
neural rod1.48e-1056
future spinal cord1.48e-1056
neural keel1.48e-1056
multi-cellular organism2.24e-10656
structure with developmental contribution from neural crest2.70e-10132
anatomical cluster6.69e-10373
anatomical conduit1.34e-09240
regional part of nervous system2.45e-0953
regional part of brain2.45e-0953
central nervous system3.76e-0981
brain4.44e-0968
future brain4.44e-0968
primary circulatory organ1.79e-0827
organ system subdivision2.69e-08223
neural plate7.39e-0882
presumptive neural plate7.39e-0882
regional part of forebrain1.14e-0741
forebrain1.14e-0741
anterior neural tube1.14e-0741
future forebrain1.14e-0741
tube1.22e-07192
heart1.26e-0724
primitive heart tube1.26e-0724
primary heart field1.26e-0724
anterior lateral plate mesoderm1.26e-0724
heart tube1.26e-0724
heart primordium1.26e-0724
cardiac mesoderm1.26e-0724
cardiogenic plate1.26e-0724
heart rudiment1.26e-0724
nervous system1.88e-0789
mesenchyme2.78e-07160
entire embryonic mesenchyme2.78e-07160
epithelium6.40e-07306
adipose tissue7.92e-0714


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
NR3C1#290838.983813998703820.002687995788940450.0147987133474513
TFAP2C#702236.485537165916130.006858951517940.0290664247345156



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.