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Coexpression cluster:C3969: Difference between revisions

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|ontology_enrichment_disease=
|ontology_enrichment_disease=
|ontology_enrichment_uberon=UBERON:0003102!9.15e-21!95;UBERON:0004119!1.74e-17!169;UBERON:0000925!1.74e-17!169;UBERON:0006595!1.74e-17!169;UBERON:0002100!1.30e-15!216;UBERON:0000475!6.06e-15!365;UBERON:0000161!1.95e-13!35;UBERON:0001007!1.16e-12!155;UBERON:0001555!1.16e-12!155;UBERON:0007026!1.16e-12!155;UBERON:0003104!2.85e-12!238;UBERON:0009142!2.85e-12!238;UBERON:0005256!1.19e-11!143;UBERON:0000468!5.89e-10!659;UBERON:0000481!1.04e-09!347;UBERON:0000165!1.22e-09!28;UBERON:0000930!1.22e-09!28;UBERON:0000467!2.58e-09!625;UBERON:0001008!3.67e-09!45;UBERON:0000480!3.76e-09!626;UBERON:0006554!8.21e-09!44;UBERON:0000077!1.17e-08!130;UBERON:0001444!2.05e-08!48;UBERON:0001004!2.07e-08!72;UBERON:0009569!2.09e-08!113;UBERON:0004921!4.13e-08!129;UBERON:0004185!4.13e-08!129;UBERON:0000166!4.49e-08!21;UBERON:0000486!1.19e-07!82;UBERON:0000922!2.33e-07!612;UBERON:0004122!3.28e-07!15;UBERON:0003064!4.21e-07!37;UBERON:0000923!7.03e-07!604;UBERON:0005291!7.03e-07!604;UBERON:0006598!7.03e-07!604;UBERON:0002532!7.03e-07!604;UBERON:0000162!7.27e-07!14;UBERON:0001353!7.27e-07!14;UBERON:0000163!7.27e-07!14;UBERON:0006866!7.27e-07!14;UBERON:0000164!7.27e-07!14;UBERON:0000931!7.27e-07!14;UBERON:0000914!8.23e-07!83;UBERON:0002329!8.23e-07!83;UBERON:0003077!8.23e-07!83;UBERON:0003059!8.23e-07!83;UBERON:0007282!8.23e-07!83;UBERON:0009618!8.23e-07!83;UBERON:0007285!8.23e-07!83;UBERON:0000464!9.45e-07!104;UBERON:0002199!9.47e-07!45;UBERON:0002416!9.47e-07!45;UBERON:0002050!9.64e-07!605;UBERON:0005423!9.64e-07!605
|ontology_enrichment_uberon=UBERON:0003102!9.15e-21!95;UBERON:0004119!1.74e-17!169;UBERON:0000925!1.74e-17!169;UBERON:0006595!1.74e-17!169;UBERON:0002100!1.30e-15!216;UBERON:0000475!6.06e-15!365;UBERON:0000161!1.95e-13!35;UBERON:0001007!1.16e-12!155;UBERON:0001555!1.16e-12!155;UBERON:0007026!1.16e-12!155;UBERON:0003104!2.85e-12!238;UBERON:0009142!2.85e-12!238;UBERON:0005256!1.19e-11!143;UBERON:0000468!5.89e-10!659;UBERON:0000481!1.04e-09!347;UBERON:0000165!1.22e-09!28;UBERON:0000930!1.22e-09!28;UBERON:0000467!2.58e-09!625;UBERON:0001008!3.67e-09!45;UBERON:0000480!3.76e-09!626;UBERON:0006554!8.21e-09!44;UBERON:0000077!1.17e-08!130;UBERON:0001444!2.05e-08!48;UBERON:0001004!2.07e-08!72;UBERON:0009569!2.09e-08!113;UBERON:0004921!4.13e-08!129;UBERON:0004185!4.13e-08!129;UBERON:0000166!4.49e-08!21;UBERON:0000486!1.19e-07!82;UBERON:0000922!2.33e-07!612;UBERON:0004122!3.28e-07!15;UBERON:0003064!4.21e-07!37;UBERON:0000923!7.03e-07!604;UBERON:0005291!7.03e-07!604;UBERON:0006598!7.03e-07!604;UBERON:0002532!7.03e-07!604;UBERON:0000162!7.27e-07!14;UBERON:0001353!7.27e-07!14;UBERON:0000163!7.27e-07!14;UBERON:0006866!7.27e-07!14;UBERON:0000164!7.27e-07!14;UBERON:0000931!7.27e-07!14;UBERON:0000914!8.23e-07!83;UBERON:0002329!8.23e-07!83;UBERON:0003077!8.23e-07!83;UBERON:0003059!8.23e-07!83;UBERON:0007282!8.23e-07!83;UBERON:0009618!8.23e-07!83;UBERON:0007285!8.23e-07!83;UBERON:0000464!9.45e-07!104;UBERON:0002199!9.47e-07!45;UBERON:0002416!9.47e-07!45;UBERON:0002050!9.64e-07!605;UBERON:0005423!9.64e-07!605
|tf_chipseq_enrich=TCF7L2#6934;3:10.7701765631373:0.000800318129839838:0.00614275190433915
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0993,0.0440463,2.58765e-05,0.249955,0.164638,0.224257,0.0935776,0.327622,0.225752,0.207791,0.0958756,0.0859274,0.056548,0.171683,0.158847,0.0406636,0.071111,0.270604,0.101021,0.222548,0.175934,0.157274,0.215705,0.252796,0.0017212,0.0750181
}}
}}

Revision as of 14:23, 5 September 2012


Full id: C3969_Prostate_Keratinocyte_liver_Small_Tracheal_Hepatocyte_Fibroblast



Phase1 CAGE Peaks

Hg19::chr1:31907100..31907130,+p@chr1:31907100..31907130
+
Hg19::chr1:31907140..31907157,+p@chr1:31907140..31907157
+
Hg19::chr1:31907237..31907260,+p@chr1:31907237..31907260
+


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><br>

Cell Type
Ontology termp-valuen
embryonic cell6.02e-16248
epithelial cell5.45e-13254
endo-epithelial cell6.55e-1143
endodermal cell8.38e-1159
ecto-epithelial cell1.97e-0933
general ecto-epithelial cell1.80e-0813
non-terminally differentiated cell2.36e-08180
animal cell1.17e-07679
eukaryotic cell1.17e-07679
somatic cell1.62e-07591
respiratory epithelial cell4.51e-0713
Uber Anatomy
Ontology termp-valuen
surface structure9.15e-2195
endoderm-derived structure1.74e-17169
endoderm1.74e-17169
presumptive endoderm1.74e-17169
trunk1.30e-15216
organism subdivision6.06e-15365
orifice1.95e-1335
digestive system1.16e-12155
digestive tract1.16e-12155
primitive gut1.16e-12155
mesenchyme2.85e-12238
entire embryonic mesenchyme2.85e-12238
trunk mesenchyme1.19e-11143
multi-cellular organism5.89e-10659
multi-tissue structure1.04e-09347
mouth1.22e-0928
stomodeum1.22e-0928
anatomical system2.58e-09625
renal system3.67e-0945
anatomical group3.76e-09626
urinary system structure8.21e-0944
mixed endoderm/mesoderm-derived structure1.17e-08130
subdivision of head2.05e-0848
respiratory system2.07e-0872
subdivision of trunk2.09e-08113
subdivision of digestive tract4.13e-08129
endodermal part of digestive tract4.13e-08129
oral opening4.49e-0821
multilaminar epithelium1.19e-0782
embryo2.33e-07612
genitourinary system3.28e-0715
intermediate mesoderm4.21e-0737
germ layer7.03e-07604
embryonic tissue7.03e-07604
presumptive structure7.03e-07604
epiblast (generic)7.03e-07604
cloaca7.27e-0714
anal region7.27e-0714
embryonic cloaca7.27e-0714
terminal part of digestive tract7.27e-0714
primitive urogenital sinus7.27e-0714
proctodeum7.27e-0714
somite8.23e-0783
paraxial mesoderm8.23e-0783
presomitic mesoderm8.23e-0783
presumptive segmental plate8.23e-0783
trunk paraxial mesoderm8.23e-0783
presumptive paraxial mesoderm8.23e-0783
anatomical space9.45e-07104
integument9.47e-0745
integumental system9.47e-0745
embryonic structure9.64e-07605
developing anatomical structure9.64e-07605


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
TCF7L2#6934310.77017656313730.0008003181298398380.00614275190433915



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.

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