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|full_id=C3876_colon_liver_Hepatocyte_choriocarcinoma_chorionic_Renal_serous
|full_id=C3876_colon_liver_Hepatocyte_choriocarcinoma_chorionic_Renal_serous
|id=C3876
|id=C3876
|ontology_enrichment_celltype=CL:0000066!1.80e-47!254;CL:0000223!1.63e-17!59;CL:0000076!9.17e-13!62;CL:0002076!2.66e-12!43;CL:0002139!1.37e-11!24;CL:0000115!1.15e-10!35;CL:0002078!7.67e-10!44;CL:0000213!1.02e-09!57;CL:0000215!1.02e-09!57;CL:0000071!2.30e-08!18;CL:0002546!2.30e-08!18
|ontology_enrichment_disease=DOID:305!4.29e-20!106;DOID:0050687!3.49e-17!143;DOID:299!7.51e-07!25
|ontology_enrichment_uberon=UBERON:0004119!1.94e-22!169;UBERON:0000925!1.94e-22!169;UBERON:0006595!1.94e-22!169;UBERON:0004921!3.09e-19!129;UBERON:0004185!3.09e-19!129;UBERON:0000477!7.96e-19!286;UBERON:0001007!1.98e-18!155;UBERON:0001555!1.98e-18!155;UBERON:0007026!1.98e-18!155;UBERON:0004111!3.24e-18!241;UBERON:0000077!8.08e-17!130;UBERON:0001041!2.09e-16!98;UBERON:0005177!1.99e-15!107;UBERON:0000064!4.94e-15!219;UBERON:0007023!9.23e-15!115;UBERON:0000025!4.89e-13!194;UBERON:0000062!1.64e-12!511;UBERON:0005911!2.52e-12!82;UBERON:0000481!3.09e-12!347;UBERON:0000468!1.61e-11!659;UBERON:0001004!1.96e-11!72;UBERON:0000483!2.17e-11!309;UBERON:0000922!3.06e-11!612;UBERON:0000119!6.77e-11!312;UBERON:0000466!1.18e-10!126;UBERON:0002050!1.84e-10!605;UBERON:0005423!1.84e-10!605;UBERON:0000923!3.05e-10!604;UBERON:0005291!3.05e-10!604;UBERON:0006598!3.05e-10!604;UBERON:0002532!3.05e-10!604;UBERON:0000467!4.83e-10!625;UBERON:0000480!5.75e-10!626;UBERON:0005172!6.28e-10!55;UBERON:0005173!6.28e-10!55;UBERON:0008947!8.59e-10!38;UBERON:0003258!8.59e-10!38;UBERON:0000065!1.07e-09!53;UBERON:0009569!1.52e-09!113;UBERON:0002365!3.27e-09!31;UBERON:0002330!3.27e-09!31;UBERON:0001048!1.23e-08!168;UBERON:0002530!1.28e-08!59;UBERON:0001986!2.30e-08!18;UBERON:0004638!2.30e-08!18;UBERON:0004852!2.30e-08!18;UBERON:0009497!2.19e-07!25;UBERON:0000015!2.19e-07!25;UBERON:0002423!2.19e-07!25;UBERON:0006235!2.19e-07!25;UBERON:0004161!2.19e-07!25;UBERON:0003929!2.30e-07!54;UBERON:0000487!2.83e-07!22;UBERON:0000924!4.44e-07!173;UBERON:0006601!4.44e-07!173;UBERON:0002417!4.47e-07!61;UBERON:0000916!4.47e-07!61;UBERON:0000072!5.13e-07!46;UBERON:0004121!5.37e-07!169;UBERON:0001049!5.85e-07!57;UBERON:0005068!5.85e-07!57;UBERON:0006241!5.85e-07!57;UBERON:0007135!5.85e-07!57
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Revision as of 14:41, 21 May 2012


Full id: C3876_colon_liver_Hepatocyte_choriocarcinoma_chorionic_Renal_serous



Phase1 CAGE Peaks

Hg19::chr1:155100342..155100359,+p1@EFNA1
Hg19::chr1:155100366..155100377,+p2@EFNA1
Hg19::chr1:155100387..155100398,+p3@EFNA1


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>disease_data<br>


Uber Anatomy
Ontology termp-valuen
endoderm-derived structure1.94e-22169
endoderm1.94e-22169
presumptive endoderm1.94e-22169
subdivision of digestive tract3.09e-19129
endodermal part of digestive tract3.09e-19129
anatomical cluster7.96e-19286
digestive system1.98e-18155
digestive tract1.98e-18155
primitive gut1.98e-18155
anatomical conduit3.24e-18241
mixed endoderm/mesoderm-derived structure8.08e-17130
foregut2.09e-1698
trunk region element1.99e-15107
organ part4.94e-15219
adult organism9.23e-15115
tube4.89e-13194
organ1.64e-12511
endo-epithelium2.52e-1282
multi-tissue structure3.09e-12347
multi-cellular organism1.61e-11659
respiratory system1.96e-1172
epithelium2.17e-11309
embryo3.06e-11612
cell layer6.77e-11312
immaterial anatomical entity1.18e-10126
embryonic structure1.84e-10605
developing anatomical structure1.84e-10605
germ layer3.05e-10604
embryonic tissue3.05e-10604
presumptive structure3.05e-10604
epiblast (generic)3.05e-10604
anatomical system4.83e-10625
anatomical group5.75e-10626
abdomen element6.28e-1055
abdominal segment element6.28e-1055
respiratory primordium8.59e-1038
endoderm of foregut8.59e-1038
respiratory tract1.07e-0953
subdivision of trunk1.52e-09113
exocrine gland3.27e-0931
exocrine system3.27e-0931
primordium1.23e-08168
gland1.28e-0859
endothelium2.30e-0818
blood vessel endothelium2.30e-0818
cardiovascular system endothelium2.30e-0818
epithelium of foregut-midgut junction2.19e-0725
anatomical boundary2.19e-0725
hepatobiliary system2.19e-0725
foregut-midgut junction2.19e-0725
septum transversum2.19e-0725
gut epithelium2.30e-0754
simple squamous epithelium2.83e-0722
ectoderm4.44e-07173
presumptive ectoderm4.44e-07173
abdominal segment of trunk4.47e-0761
abdomen4.47e-0761
segment of respiratory tract5.13e-0746
ectoderm-derived structure5.37e-07169
neural tube5.85e-0757
neural rod5.85e-0757
future spinal cord5.85e-0757
neural keel5.85e-0757
Disease
Ontology termp-valuen
carcinoma4.29e-20106
cell type cancer3.49e-17143
adenocarcinoma7.51e-0725


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


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.