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Coexpression cluster:C3226: Difference between revisions

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|ontology_enrichment_disease=
|ontology_enrichment_disease=
|ontology_enrichment_uberon=UBERON:0004111!5.39e-29!241;UBERON:0000025!2.91e-26!194;UBERON:0000119!2.19e-25!312;UBERON:0000483!2.96e-25!309;UBERON:0000477!1.31e-23!286;UBERON:0000468!2.98e-22!659;UBERON:0000475!1.33e-19!365;UBERON:0000467!2.50e-19!625;UBERON:0000480!5.65e-19!626;UBERON:0002049!8.47e-17!79;UBERON:0007798!8.47e-17!79;UBERON:0000055!1.33e-16!69;UBERON:0001017!3.29e-15!82;UBERON:0003914!3.72e-15!118;UBERON:0004872!7.54e-15!84;UBERON:0005743!8.73e-15!86;UBERON:0001981!3.94e-14!60;UBERON:0007500!3.94e-14!60;UBERON:0004537!3.94e-14!60;UBERON:0006965!3.94e-14!60;UBERON:0000073!1.04e-12!94;UBERON:0001016!1.04e-12!94;UBERON:0001009!1.58e-12!113;UBERON:0000955!3.46e-12!69;UBERON:0006238!3.46e-12!69;UBERON:0001049!9.66e-12!57;UBERON:0005068!9.66e-12!57;UBERON:0006241!9.66e-12!57;UBERON:0007135!9.66e-12!57;UBERON:0004535!1.10e-11!110;UBERON:0002616!1.66e-11!59;UBERON:0000064!3.24e-11!219;UBERON:0000922!5.49e-11!612;UBERON:0004121!6.91e-11!169;UBERON:0000481!8.65e-11!347;UBERON:0002050!1.45e-10!605;UBERON:0005423!1.45e-10!605;UBERON:0000923!2.20e-10!604;UBERON:0005291!2.20e-10!604;UBERON:0006598!2.20e-10!604;UBERON:0002532!2.20e-10!604;UBERON:0007023!2.92e-10!115;UBERON:0000924!3.68e-10!173;UBERON:0006601!3.68e-10!173;UBERON:0003075!7.39e-10!86;UBERON:0007284!7.39e-10!86;UBERON:0001893!1.34e-09!34;UBERON:0003080!1.77e-09!42;UBERON:0000490!2.29e-09!138;UBERON:0002791!3.64e-09!33;UBERON:0002780!4.04e-09!41;UBERON:0001890!4.04e-09!41;UBERON:0006240!4.04e-09!41;UBERON:0002020!4.49e-09!34;UBERON:0003528!4.49e-09!34;UBERON:0001637!4.64e-09!42;UBERON:0003509!4.64e-09!42;UBERON:0004572!4.64e-09!42;UBERON:0001869!5.83e-09!32;UBERON:0002346!7.64e-09!90;UBERON:0000956!3.05e-08!25;UBERON:0000203!3.05e-08!25;UBERON:0001986!7.08e-08!18;UBERON:0004638!7.08e-08!18;UBERON:0004852!7.08e-08!18;UBERON:0000033!7.70e-08!123;UBERON:0002100!9.97e-08!216;UBERON:0000153!2.55e-07!129;UBERON:0007811!2.55e-07!129;UBERON:0002619!4.52e-07!22;UBERON:0001950!4.60e-07!20;UBERON:0000487!5.56e-07!22
|ontology_enrichment_uberon=UBERON:0004111!5.39e-29!241;UBERON:0000025!2.91e-26!194;UBERON:0000119!2.19e-25!312;UBERON:0000483!2.96e-25!309;UBERON:0000477!1.31e-23!286;UBERON:0000468!2.98e-22!659;UBERON:0000475!1.33e-19!365;UBERON:0000467!2.50e-19!625;UBERON:0000480!5.65e-19!626;UBERON:0002049!8.47e-17!79;UBERON:0007798!8.47e-17!79;UBERON:0000055!1.33e-16!69;UBERON:0001017!3.29e-15!82;UBERON:0003914!3.72e-15!118;UBERON:0004872!7.54e-15!84;UBERON:0005743!8.73e-15!86;UBERON:0001981!3.94e-14!60;UBERON:0007500!3.94e-14!60;UBERON:0004537!3.94e-14!60;UBERON:0006965!3.94e-14!60;UBERON:0000073!1.04e-12!94;UBERON:0001016!1.04e-12!94;UBERON:0001009!1.58e-12!113;UBERON:0000955!3.46e-12!69;UBERON:0006238!3.46e-12!69;UBERON:0001049!9.66e-12!57;UBERON:0005068!9.66e-12!57;UBERON:0006241!9.66e-12!57;UBERON:0007135!9.66e-12!57;UBERON:0004535!1.10e-11!110;UBERON:0002616!1.66e-11!59;UBERON:0000064!3.24e-11!219;UBERON:0000922!5.49e-11!612;UBERON:0004121!6.91e-11!169;UBERON:0000481!8.65e-11!347;UBERON:0002050!1.45e-10!605;UBERON:0005423!1.45e-10!605;UBERON:0000923!2.20e-10!604;UBERON:0005291!2.20e-10!604;UBERON:0006598!2.20e-10!604;UBERON:0002532!2.20e-10!604;UBERON:0007023!2.92e-10!115;UBERON:0000924!3.68e-10!173;UBERON:0006601!3.68e-10!173;UBERON:0003075!7.39e-10!86;UBERON:0007284!7.39e-10!86;UBERON:0001893!1.34e-09!34;UBERON:0003080!1.77e-09!42;UBERON:0000490!2.29e-09!138;UBERON:0002791!3.64e-09!33;UBERON:0002780!4.04e-09!41;UBERON:0001890!4.04e-09!41;UBERON:0006240!4.04e-09!41;UBERON:0002020!4.49e-09!34;UBERON:0003528!4.49e-09!34;UBERON:0001637!4.64e-09!42;UBERON:0003509!4.64e-09!42;UBERON:0004572!4.64e-09!42;UBERON:0001869!5.83e-09!32;UBERON:0002346!7.64e-09!90;UBERON:0000956!3.05e-08!25;UBERON:0000203!3.05e-08!25;UBERON:0001986!7.08e-08!18;UBERON:0004638!7.08e-08!18;UBERON:0004852!7.08e-08!18;UBERON:0000033!7.70e-08!123;UBERON:0002100!9.97e-08!216;UBERON:0000153!2.55e-07!129;UBERON:0007811!2.55e-07!129;UBERON:0002619!4.52e-07!22;UBERON:0001950!4.60e-07!20;UBERON:0000487!5.56e-07!22
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}}
}}

Revision as of 14:02, 5 September 2012


Full id: C3226_Endothelial_hepatic_Renal_Urothelial_Ewing_Preadipocyte_Fibroblast



Phase1 CAGE Peaks

Hg19::chr12:106532657..106532694,-p2@NUAK1
Hg19::chr12:106532697..106532718,-p4@NUAK1
Hg19::chr12:106532724..106532740,-p1@NUAK1


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
anatomical conduit5.39e-29241
tube2.91e-26194
cell layer2.19e-25312
epithelium2.96e-25309
anatomical cluster1.31e-23286
multi-cellular organism2.98e-22659
organism subdivision1.33e-19365
anatomical system2.50e-19625
anatomical group5.65e-19626
vasculature8.47e-1779
vascular system8.47e-1779
vessel1.33e-1669
central nervous system3.29e-1582
epithelial tube3.72e-15118
splanchnic layer of lateral plate mesoderm7.54e-1584
blood vessel3.94e-1460
epithelial tube open at both ends3.94e-1460
blood vasculature3.94e-1460
vascular cord3.94e-1460
regional part of nervous system1.04e-1294
nervous system1.04e-1294
circulatory system1.58e-12113
brain3.46e-1269
future brain3.46e-1269
neural tube9.66e-1257
neural rod9.66e-1257
future spinal cord9.66e-1257
neural keel9.66e-1257
cardiovascular system1.10e-11110
regional part of brain1.66e-1159
organ part3.24e-11219
embryo5.49e-11612
ectoderm-derived structure6.91e-11169
multi-tissue structure8.65e-11347
embryonic structure1.45e-10605
developing anatomical structure1.45e-10605
germ layer2.20e-10604
embryonic tissue2.20e-10604
presumptive structure2.20e-10604
epiblast (generic)2.20e-10604
adult organism2.92e-10115
ectoderm3.68e-10173
presumptive ectoderm3.68e-10173
neural plate7.39e-1086
presumptive neural plate7.39e-1086
telencephalon1.34e-0934
anterior neural tube1.77e-0942
unilaminar epithelium2.29e-09138
regional part of telencephalon3.64e-0933
regional part of forebrain4.04e-0941
forebrain4.04e-0941
future forebrain4.04e-0941
gray matter4.49e-0934
brain grey matter4.49e-0934
artery4.64e-0942
arterial blood vessel4.64e-0942
arterial system4.64e-0942
cerebral hemisphere5.83e-0932
neurectoderm7.64e-0990
cerebral cortex3.05e-0825
pallium3.05e-0825
endothelium7.08e-0818
blood vessel endothelium7.08e-0818
cardiovascular system endothelium7.08e-0818
head7.70e-08123
trunk9.97e-08216
anterior region of body2.55e-07129
craniocervical region2.55e-07129
regional part of cerebral cortex4.52e-0722
neocortex4.60e-0720
simple squamous epithelium5.56e-0722


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
CHD2#1106310.34402283411690.0009033701102746880.00658710262842827
E2F1#186934.907389214879320.008460985347239390.0323909258707648



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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