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Coexpression cluster:C638: Difference between revisions

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|ontology_enrichment_disease=
|ontology_enrichment_disease=
|ontology_enrichment_uberon=UBERON:0000914!9.78e-29!83;UBERON:0002329!9.78e-29!83;UBERON:0003077!9.78e-29!83;UBERON:0003059!9.78e-29!83;UBERON:0007282!9.78e-29!83;UBERON:0009618!9.78e-29!83;UBERON:0007285!9.78e-29!83;UBERON:0004290!2.17e-27!70;UBERON:0002385!1.34e-25!63;UBERON:0001015!1.34e-25!63;UBERON:0000383!1.34e-25!63;UBERON:0001134!4.62e-25!61;UBERON:0002036!4.62e-25!61;UBERON:0003082!4.62e-25!61;UBERON:0000486!2.75e-23!82;UBERON:0005256!6.87e-22!143;UBERON:0000481!3.53e-19!347;UBERON:0003104!4.94e-19!238;UBERON:0009142!4.94e-19!238;UBERON:0002100!4.26e-17!216;UBERON:0000468!4.40e-17!659;UBERON:0000475!1.15e-15!365;UBERON:0004872!2.66e-14!84;UBERON:0001637!2.34e-13!42;UBERON:0003509!2.34e-13!42;UBERON:0004572!2.34e-13!42;UBERON:0001981!9.13e-13!60;UBERON:0007500!9.13e-13!60;UBERON:0004537!9.13e-13!60;UBERON:0006965!9.13e-13!60;UBERON:0000490!1.36e-12!138;UBERON:0002049!3.37e-12!79;UBERON:0007798!3.37e-12!79;UBERON:0000467!7.16e-12!625;UBERON:0000926!1.01e-11!448;UBERON:0004120!1.01e-11!448;UBERON:0006603!1.01e-11!448;UBERON:0000922!1.19e-11!612;UBERON:0000480!1.49e-11!626;UBERON:0002050!8.47e-11!605;UBERON:0005423!8.47e-11!605;UBERON:0004573!9.23e-11!33;UBERON:0004571!9.23e-11!33;UBERON:0003914!1.03e-10!118;UBERON:0000923!1.73e-10!604;UBERON:0005291!1.73e-10!604;UBERON:0006598!1.73e-10!604;UBERON:0002532!1.73e-10!604;UBERON:0000055!4.07e-10!69;UBERON:0001009!1.54e-09!113;UBERON:0004535!4.91e-09!110;UBERON:0003102!1.14e-08!95;UBERON:0000119!1.15e-08!312;UBERON:0000483!1.43e-08!309;UBERON:0007100!1.27e-07!27;UBERON:0000477!3.58e-07!286;UBERON:0000948!4.19e-07!24;UBERON:0005498!4.19e-07!24;UBERON:0004140!4.19e-07!24;UBERON:0009881!4.19e-07!24;UBERON:0004141!4.19e-07!24;UBERON:0003084!4.19e-07!24;UBERON:0007005!4.19e-07!24;UBERON:0004139!4.19e-07!24;UBERON:0004291!4.19e-07!24;UBERON:0001135!8.92e-07!15
|ontology_enrichment_uberon=UBERON:0000914!9.78e-29!83;UBERON:0002329!9.78e-29!83;UBERON:0003077!9.78e-29!83;UBERON:0003059!9.78e-29!83;UBERON:0007282!9.78e-29!83;UBERON:0009618!9.78e-29!83;UBERON:0007285!9.78e-29!83;UBERON:0004290!2.17e-27!70;UBERON:0002385!1.34e-25!63;UBERON:0001015!1.34e-25!63;UBERON:0000383!1.34e-25!63;UBERON:0001134!4.62e-25!61;UBERON:0002036!4.62e-25!61;UBERON:0003082!4.62e-25!61;UBERON:0000486!2.75e-23!82;UBERON:0005256!6.87e-22!143;UBERON:0000481!3.53e-19!347;UBERON:0003104!4.94e-19!238;UBERON:0009142!4.94e-19!238;UBERON:0002100!4.26e-17!216;UBERON:0000468!4.40e-17!659;UBERON:0000475!1.15e-15!365;UBERON:0004872!2.66e-14!84;UBERON:0001637!2.34e-13!42;UBERON:0003509!2.34e-13!42;UBERON:0004572!2.34e-13!42;UBERON:0001981!9.13e-13!60;UBERON:0007500!9.13e-13!60;UBERON:0004537!9.13e-13!60;UBERON:0006965!9.13e-13!60;UBERON:0000490!1.36e-12!138;UBERON:0002049!3.37e-12!79;UBERON:0007798!3.37e-12!79;UBERON:0000467!7.16e-12!625;UBERON:0000926!1.01e-11!448;UBERON:0004120!1.01e-11!448;UBERON:0006603!1.01e-11!448;UBERON:0000922!1.19e-11!612;UBERON:0000480!1.49e-11!626;UBERON:0002050!8.47e-11!605;UBERON:0005423!8.47e-11!605;UBERON:0004573!9.23e-11!33;UBERON:0004571!9.23e-11!33;UBERON:0003914!1.03e-10!118;UBERON:0000923!1.73e-10!604;UBERON:0005291!1.73e-10!604;UBERON:0006598!1.73e-10!604;UBERON:0002532!1.73e-10!604;UBERON:0000055!4.07e-10!69;UBERON:0001009!1.54e-09!113;UBERON:0004535!4.91e-09!110;UBERON:0003102!1.14e-08!95;UBERON:0000119!1.15e-08!312;UBERON:0000483!1.43e-08!309;UBERON:0007100!1.27e-07!27;UBERON:0000477!3.58e-07!286;UBERON:0000948!4.19e-07!24;UBERON:0005498!4.19e-07!24;UBERON:0004140!4.19e-07!24;UBERON:0009881!4.19e-07!24;UBERON:0004141!4.19e-07!24;UBERON:0003084!4.19e-07!24;UBERON:0007005!4.19e-07!24;UBERON:0004139!4.19e-07!24;UBERON:0004291!4.19e-07!24;UBERON:0001135!8.92e-07!15
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}}
}}

Revision as of 12:56, 5 September 2012


Full id: C638_skeletal_tongue_Adipocyte_diaphragm_penis_throat_Smooth



Phase1 CAGE Peaks

Hg19::chr9:35684475..35684520,+p@chr9:35684475..35684520
+
Hg19::chr9:35684538..35684558,-p@chr9:35684538..35684558
-
Hg19::chr9:35685273..35685313,+p@chr9:35685273..35685313
+
Hg19::chr9:35685418..35685431,+p@chr9:35685418..35685431
+
Hg19::chr9:35685445..35685517,+p@chr9:35685445..35685517
+
Hg19::chr9:35685537..35685548,-p9@TPM2
Hg19::chr9:35685631..35685657,+p@chr9:35685631..35685657
+
Hg19::chr9:35685667..35685687,-p7@TPM2
Hg19::chr9:35685751..35685774,-p5@TPM2
Hg19::chr9:35689148..35689192,+p@chr9:35689148..35689192
+
Hg19::chr9:35689172..35689190,-p@chr9:35689172..35689190
-
Hg19::chr9:35689196..35689218,-p@chr9:35689196..35689218
-
Hg19::chr9:35689248..35689267,-p@chr9:35689248..35689267
-
Hg19::chr9:35689915..35689930,-p1@TPM2


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>

Uber Anatomy
Ontology termp-valuen
somite9.78e-2983
paraxial mesoderm9.78e-2983
presomitic mesoderm9.78e-2983
presumptive segmental plate9.78e-2983
trunk paraxial mesoderm9.78e-2983
presumptive paraxial mesoderm9.78e-2983
dermomyotome2.17e-2770
muscle tissue1.34e-2563
musculature1.34e-2563
musculature of body1.34e-2563
skeletal muscle tissue4.62e-2561
striated muscle tissue4.62e-2561
myotome4.62e-2561
multilaminar epithelium2.75e-2382
trunk mesenchyme6.87e-22143
multi-tissue structure3.53e-19347
mesenchyme4.94e-19238
entire embryonic mesenchyme4.94e-19238
trunk4.26e-17216
multi-cellular organism4.40e-17659
organism subdivision1.15e-15365
splanchnic layer of lateral plate mesoderm2.66e-1484
artery2.34e-1342
arterial blood vessel2.34e-1342
arterial system2.34e-1342
blood vessel9.13e-1360
epithelial tube open at both ends9.13e-1360
blood vasculature9.13e-1360
vascular cord9.13e-1360
unilaminar epithelium1.36e-12138
vasculature3.37e-1279
vascular system3.37e-1279
anatomical system7.16e-12625
mesoderm1.01e-11448
mesoderm-derived structure1.01e-11448
presumptive mesoderm1.01e-11448
embryo1.19e-11612
anatomical group1.49e-11626
embryonic structure8.47e-11605
developing anatomical structure8.47e-11605
systemic artery9.23e-1133
systemic arterial system9.23e-1133
epithelial tube1.03e-10118
germ layer1.73e-10604
embryonic tissue1.73e-10604
presumptive structure1.73e-10604
epiblast (generic)1.73e-10604
vessel4.07e-1069
circulatory system1.54e-09113
cardiovascular system4.91e-09110
surface structure1.14e-0895
cell layer1.15e-08312
epithelium1.43e-08309
primary circulatory organ1.27e-0727
anatomical cluster3.58e-07286
heart4.19e-0724
primitive heart tube4.19e-0724
primary heart field4.19e-0724
anterior lateral plate mesoderm4.19e-0724
heart tube4.19e-0724
heart primordium4.19e-0724
cardiac mesoderm4.19e-0724
cardiogenic plate4.19e-0724
heart rudiment4.19e-0724
smooth muscle tissue8.92e-0715


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
TFAP2A#702044.719609820869990.008221727346191040.0324491339395679



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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