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Coexpression cluster:C1277

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Full id: C1277_Hepatocyte_mature_mesenchymal_smooth_bladder_normal_cholangiocellular



Phase1 CAGE Peaks

Hg19::chr5:52083909..52083927,+p7@PELO
Hg19::chr5:52083929..52083940,+p12@PELO
Hg19::chr5:52083991..52084021,+p3@ITGA1
Hg19::chr5:52084023..52084051,+p2@ITGA1
Hg19::chr5:52084059..52084086,+p4@ITGA1
Hg19::chr5:52084087..52084115,+p5@ITGA1
Hg19::chr5:52084126..52084133,+p8@ITGA1


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:0045123cellular extravasation0.0155415249616414
GO:0030593neutrophil chemotaxis0.0223346942055352
GO:0005518collagen binding0.0223346942055352
GO:0030595leukocyte chemotaxis0.0223346942055352
GO:0050900leukocyte migration0.0240797902081608
GO:0009897external side of plasma membrane0.0305050789062747
GO:0008305integrin complex0.0305050789062747
GO:0007229integrin-mediated signaling pathway0.038793191786861
GO:0007160cell-matrix adhesion0.038793191786861
GO:0031589cell-substrate adhesion0.038793191786861
GO:0043235receptor complex0.038793191786861
GO:0042330taxis0.0409869718598991
GO:0006935chemotaxis0.0409869718598991
GO:0009986cell surface0.0409869718598991
GO:0007626locomotory behavior0.0467614554761341



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><br>uberon_data<br><br>


Uber Anatomy
Ontology termp-valuen
adult organism3.49e-13114
multi-tissue structure4.99e-12342
anatomical cluster8.30e-11373
multi-cellular organism6.27e-10656
digestive system8.25e-10145
digestive tract8.25e-10145
primitive gut8.25e-10145
subdivision of digestive tract9.24e-10118
mesenchyme3.32e-08160
entire embryonic mesenchyme3.32e-08160
endoderm-derived structure4.05e-08160
endoderm4.05e-08160
presumptive endoderm4.05e-08160
primordium7.46e-08160
liver1.69e-0719
digestive gland1.69e-0719
liver bud1.69e-0719
trunk mesenchyme2.39e-07122
organ system subdivision2.81e-07223
sac4.22e-0726
trunk6.55e-07199
digestive tract diverticulum6.73e-0723
endocrine gland7.92e-0735
anatomical system9.39e-07624


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
CEBPB#105177.971147625824824.88663622402061e-072.30200902390838e-05
CTCF#1066475.360256373075037.86114662284756e-060.00022249601413105
E2F1#186974.907389214879321.45832274679793e-050.000347017018347754
E2F6#187675.017155731697391.24910426162553e-050.000308331836397799
EP300#203376.77394172622321.52695018318475e-065.86729765201002e-05
FOXA2#3170724.63046375266521.81353313360781e-101.89214372568298e-08
HNF4A#3172723.13229036295372.81434373816722e-102.86199849727796e-08
HNF4G#3174728.75342252644686.13483972627905e-116.8379565226559e-09
POLR2A#543072.147453176558070.004747636447610280.0223582271250381
RAD21#588557.39645278246880.0001491014505228370.00192341976175328
SMARCB1#6598718.25271578115741.4786181847889e-091.31425876256313e-07
SMC3#9126510.74638060352352.42943476743625e-050.000527171696813369
SP1#666775.69838137814095.12280185510121e-060.000157358912630857
SRF#6722713.79717826216781.04914736064956e-087.9113286064173e-07
TAF1#687273.343046285745290.0002142336319622450.00246848480676356
TFAP2C#7022710.80922860986025.79365976833206e-083.61459995546495e-06
YY1#752874.911170749853861.45048003565243e-050.000345623281869732
ZNF263#1012778.221841637010683.93423095812578e-071.91021453759041e-05



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.