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Coexpression cluster:C1197: Difference between revisions

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|ontology_enrichment_disease=DOID:305!1.19e-13!106;DOID:0050687!6.45e-09!143;DOID:299!6.47e-09!25;DOID:7!3.74e-07!39
|ontology_enrichment_disease=DOID:305!1.19e-13!106;DOID:0050687!6.45e-09!143;DOID:299!6.47e-09!25;DOID:7!3.74e-07!39
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}}
}}

Revision as of 16:59, 8 August 2012


Full id: C1197_hepatoma_Hepatocyte_liver_argyrophil_hepatocellular_gastrointestinal_mesothelioma



Phase1 CAGE Peaks

Hg19::chr14:23445892..23445897,-p17@AJUBA
Hg19::chr14:23445927..23445936,-p15@AJUBA
Hg19::chr16:52417646..52417654,-p@chr16:52417646..52417654
-
Hg19::chr2:73248062..73248100,-p21@SFXN5
Hg19::chr5:147209673..147209678,-p@chr5:147209673..147209678
-
Hg19::chr6:50061315..50061323,+p1@ENST00000415106
Hg19::chr9:116840728..116840744,-p2@AMBP


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:0030568plasmin inhibitor activity0.00260500985625729
GO:0046904calcium oxalate binding0.00260500985625729
GO:0019862IgA binding0.00260500985625729
GO:0019855calcium channel inhibitor activity0.00260500985625729
GO:0046329negative regulation of JNK cascade0.00260500985625729
GO:0042167heme catabolic process0.00260500985625729
GO:0030304trypsin inhibitor activity0.00260500985625729
GO:0046149pigment catabolic process0.00260500985625729
GO:0006787porphyrin catabolic process0.00347324422754211
GO:0033015tetrapyrrole catabolic process0.00347324422754211
GO:0050777negative regulation of immune response0.00496141229839008
GO:0002683negative regulation of immune system process0.00496141229839008
GO:0008200ion channel inhibitor activity0.00496141229839008
GO:0016248channel inhibitor activity0.00496141229839008
GO:0005246calcium channel regulator activity0.0050936416448709
GO:0019865immunoglobulin binding0.00694536373294039
GO:0046328regulation of JNK cascade0.00767588960040256
GO:0042168heme metabolic process0.00767588960040256
GO:0018298protein-chromophore linkage0.00767588960040256
GO:0051241negative regulation of multicellular organismal process0.00868055438216479
GO:0006778porphyrin metabolic process0.00991990324056249
GO:0033013tetrapyrrole metabolic process0.0108678033134421
GO:0016247channel regulator activity0.0108678033134421
GO:0042440pigment metabolic process0.012149734272869
GO:0051187cofactor catabolic process0.0138837746380827
GO:0019748secondary metabolic process0.0141501450216093
GO:0006826iron ion transport0.0146535844609547
GO:0007254JNK cascade0.01611153515917
GO:0031098stress-activated protein kinase signaling pathway0.0162732133377396
GO:0007565female pregnancy0.018734537648372
GO:0050776regulation of immune response0.0206109159829187
GO:0002682regulation of immune system process0.0206109159829187
GO:0032403protein complex binding0.0206109159829187
GO:0000041transition metal ion transport0.0206109159829187
GO:0009968negative regulation of signal transduction0.0206109159829187
GO:0046483heterocycle metabolic process0.0250383882725595
GO:0000165MAPKKK cascade0.0281013347524844
GO:0042803protein homodimerization activity0.0288177222531866
GO:0004867serine-type endopeptidase inhibitor activity0.0298515414307917
GO:0006810transport0.0406471491569161
GO:0015674di-, tri-valent inorganic cation transport0.0406471491569161
GO:0004866endopeptidase inhibitor activity0.0406471491569161
GO:0051234establishment of localization0.0406471491569161
GO:0030414protease inhibitor activity0.0418333476446704
GO:0051239regulation of multicellular organismal process0.042588301530179
GO:0020037heme binding0.0427626175573073
GO:0046906tetrapyrrole binding0.0427626175573073
GO:0051179localization0.0427626175573073
GO:0022414reproductive process0.043047415010481
GO:0051704multi-organism process0.046040255562797
GO:0051186cofactor metabolic process0.046486109454568
GO:0042802identical protein binding0.0477151929368722
GO:0046983protein dimerization activity0.0477151929368722
GO:0007243protein kinase cascade0.0481040101179392



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>disease_data<br>


Cell Type
Ontology termp-valuen
epithelial cell1.56e-10254
metabolising cell6.11e-0912
endopolyploid cell6.11e-0912
parenchymal cell6.11e-0912
polyploid cell6.11e-0912
hepatocyte6.11e-0912
Uber Anatomy
Ontology termp-valuen
hepatic diverticulum1.36e-1322
liver primordium1.36e-1322
digestive system3.35e-13155
digestive tract3.35e-13155
primitive gut3.35e-13155
epithelium of foregut-midgut junction8.31e-1325
anatomical boundary8.31e-1325
hepatobiliary system8.31e-1325
foregut-midgut junction8.31e-1325
septum transversum8.31e-1325
digestive tract diverticulum1.05e-1223
gut epithelium5.65e-1254
subdivision of digestive tract7.27e-12129
endodermal part of digestive tract7.27e-12129
liver2.59e-1119
digestive gland2.59e-1119
liver bud2.59e-1119
epithelial sac3.75e-1125
endoderm-derived structure6.46e-11169
endoderm6.46e-11169
presumptive endoderm6.46e-11169
abdomen element7.44e-1155
abdominal segment element7.44e-1155
endo-epithelium1.79e-1082
sac1.80e-1026
immune organ6.35e-1026
abdominal segment of trunk1.97e-0961
abdomen1.97e-0961
endocrine gland4.43e-0935
primordium4.78e-08168
trunk region element7.13e-08107
foregut8.26e-0898
mixed endoderm/mesoderm-derived structure1.34e-07130
immaterial anatomical entity2.20e-07126
multi-tissue structure2.59e-07347
endocrine system2.88e-0745
Disease
Ontology termp-valuen
carcinoma1.19e-13106
cell type cancer6.45e-09143
adenocarcinoma6.47e-0925
disease of anatomical entity3.74e-0739


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)

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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


No analysis results for this cluster

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.