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Coexpression cluster:C1140: Difference between revisions

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|tf_chipseq_enrich=CEBPB#1051;5:5.69367687558915:0.000523272514554218:0.00453188972116493!EBF1#1879;5:6.36176203326358:0.000307843991861182:0.00316945176123718!EP300#2033;7:6.7739417262232:1.52695018318475e-06:5.85437408889987e-05!FOXA1#3169;6:9.49835978518753:3.4851329158676e-06:0.000115844620178325!FOXA2#3170;6:21.1118260737131:3.02035985915038e-08:2.04567680499226e-06!HDAC2#3066;5:9.58258588330447:4.24859153994197e-05:0.000759792212054793!HNF4G#3174;7:28.7534225264468:6.13483972627905e-11:6.83066659032897e-09!SP1#6667;7:5.6983813781409:5.12280185510121e-06:0.000157174002040222!TBP#6908;6:3.17723201751119:0.00207411205185266:0.0120163193311943
|tf_chipseq_enrich=CEBPB#1051;5:5.69367687558915:0.000523272514554218:0.00453188972116493!EBF1#1879;5:6.36176203326358:0.000307843991861182:0.00316945176123718!EP300#2033;7:6.7739417262232:1.52695018318475e-06:5.85437408889987e-05!FOXA1#3169;6:9.49835978518753:3.4851329158676e-06:0.000115844620178325!FOXA2#3170;6:21.1118260737131:3.02035985915038e-08:2.04567680499226e-06!HDAC2#3066;5:9.58258588330447:4.24859153994197e-05:0.000759792212054793!HNF4G#3174;7:28.7534225264468:6.13483972627905e-11:6.83066659032897e-09!SP1#6667;7:5.6983813781409:5.12280185510121e-06:0.000157174002040222!TBP#6908;6:3.17723201751119:0.00207411205185266:0.0120163193311943
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}}
}}

Revision as of 14:42, 26 November 2012


Full id: C1140_hepatocellular_B_small_gastrointestinal_argyrophil_liver_temporal



Phase1 CAGE Peaks

Hg19::chr11:22696343..22696354,+p18@GAS2
Hg19::chr2:37086230..37086242,+p@chr2:37086230..37086242
+
Hg19::chr7:34797827..34797851,-p1@AAA1
Hg19::chr7:34797852..34797863,-p2@AAA1
Hg19::chr7:34797868..34797879,-p4@AAA1
Hg19::chr7:34797894..34797905,-p3@AAA1
Hg19::chr7:34797912..34797921,-p5@AAA1


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:0005884actin filament0.0132903567643942
GO:0008360regulation of cell shape0.0132903567643942
GO:0022603regulation of anatomical structure morphogenesis0.0132903567643942
GO:0022604regulation of cell morphogenesis0.0132903567643942
GO:0007050cell cycle arrest0.0255681149181679
GO:0045786negative regulation of progression through cell cycle0.0426737985904358
GO:0050793regulation of developmental process0.0426737985904358
GO:0015629actin cytoskeleton0.0454403626515954
GO:0000074regulation of progression through cell cycle0.0454403626515954
GO:0051726regulation of cell cycle0.0454403626515954



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
metabolising cell3.00e-1312
endopolyploid cell3.00e-1312
parenchymal cell3.00e-1312
polyploid cell3.00e-1312
hepatocyte3.00e-1312
epithelial cell of cervix1.71e-092
lymphocyte of B lineage7.03e-0724
pro-B cell7.03e-0724
Uber Anatomy
Ontology termp-valuen
uterine epithelium1.71e-092
cervix epithelium1.71e-092
liver1.38e-0819
digestive gland1.38e-0819
liver bud1.38e-0819
abdomen element9.85e-0854
abdominal segment element9.85e-0854
hepatic diverticulum1.73e-0722
liver primordium1.73e-0722
digestive tract diverticulum3.48e-0723
abdominal segment of trunk5.89e-0760
abdomen5.89e-0760


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#105155.693676875589150.0005232725145542180.00453188972116493
EBF1#187956.361762033263580.0003078439918611820.00316945176123718
EP300#203376.77394172622321.52695018318475e-065.85437408889987e-05
FOXA1#316969.498359785187533.4851329158676e-060.000115844620178325
FOXA2#3170621.11182607371313.02035985915038e-082.04567680499226e-06
HDAC2#306659.582585883304474.24859153994197e-050.000759792212054793
HNF4G#3174728.75342252644686.13483972627905e-116.83066659032897e-09
SP1#666775.69838137814095.12280185510121e-060.000157174002040222
TBP#690863.177232017511190.002074112051852660.0120163193311943



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.