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Coexpression cluster:C1346: Difference between revisions

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|ontology_enrichment_disease=
|ontology_enrichment_disease=
|ontology_enrichment_uberon=UBERON:0007023!1.94e-45!115;UBERON:0004111!3.29e-27!241;UBERON:0000477!4.94e-24!286;UBERON:0000025!9.26e-21!194;UBERON:0001049!9.10e-20!57;UBERON:0005068!9.10e-20!57;UBERON:0006241!9.10e-20!57;UBERON:0007135!9.10e-20!57;UBERON:0000119!2.64e-17!312;UBERON:0000483!3.88e-17!309;UBERON:0003080!5.27e-16!42;UBERON:0002616!9.04e-16!59;UBERON:0000467!1.56e-15!625;UBERON:0000480!2.34e-15!626;UBERON:0002780!2.64e-15!41;UBERON:0001890!2.64e-15!41;UBERON:0006240!2.64e-15!41;UBERON:0000468!4.38e-15!659;UBERON:0001017!5.56e-15!82;UBERON:0001986!5.77e-15!18;UBERON:0004638!5.77e-15!18;UBERON:0004852!5.77e-15!18;UBERON:0003075!1.68e-14!86;UBERON:0007284!1.68e-14!86;UBERON:0000955!3.48e-14!69;UBERON:0006238!3.48e-14!69;UBERON:0005743!4.16e-14!86;UBERON:0002346!2.57e-13!90;UBERON:0002020!1.86e-12!34;UBERON:0003528!1.86e-12!34;UBERON:0001893!2.70e-12!34;UBERON:0002791!6.68e-12!33;UBERON:0000487!1.02e-11!22;UBERON:0000073!1.68e-11!94;UBERON:0001016!1.68e-11!94;UBERON:0001869!1.73e-11!32;UBERON:0002619!6.94e-11!22;UBERON:0000475!2.88e-10!365;UBERON:0006914!5.69e-10!25;UBERON:0000481!5.74e-10!347;UBERON:0001950!6.23e-10!20;UBERON:0004872!1.24e-09!84;UBERON:0000055!1.62e-09!69;UBERON:0000922!3.47e-09!612;UBERON:0000064!3.70e-09!219;UBERON:0000062!4.75e-09!511;UBERON:0002050!5.46e-09!605;UBERON:0005423!5.46e-09!605;UBERON:0000153!6.25e-09!129;UBERON:0007811!6.25e-09!129;UBERON:0003056!6.85e-09!61;UBERON:0000923!1.13e-08!604;UBERON:0005291!1.13e-08!604;UBERON:0006598!1.13e-08!604;UBERON:0002532!1.13e-08!604;UBERON:0000956!1.33e-08!25;UBERON:0000203!1.33e-08!25;UBERON:0004121!2.04e-08!169;UBERON:0003103!2.19e-08!69;UBERON:0000033!6.15e-08!123;UBERON:0000924!6.51e-08!173;UBERON:0006601!6.51e-08!173;UBERON:0003915!8.45e-08!9;UBERON:0004700!8.45e-08!9;UBERON:0001917!8.45e-08!9;UBERON:0002465!9.76e-08!10;UBERON:0002049!1.37e-07!79;UBERON:0007798!1.37e-07!79;UBERON:0003914!5.40e-07!118
|ontology_enrichment_uberon=UBERON:0007023!1.94e-45!115;UBERON:0004111!3.29e-27!241;UBERON:0000477!4.94e-24!286;UBERON:0000025!9.26e-21!194;UBERON:0001049!9.10e-20!57;UBERON:0005068!9.10e-20!57;UBERON:0006241!9.10e-20!57;UBERON:0007135!9.10e-20!57;UBERON:0000119!2.64e-17!312;UBERON:0000483!3.88e-17!309;UBERON:0003080!5.27e-16!42;UBERON:0002616!9.04e-16!59;UBERON:0000467!1.56e-15!625;UBERON:0000480!2.34e-15!626;UBERON:0002780!2.64e-15!41;UBERON:0001890!2.64e-15!41;UBERON:0006240!2.64e-15!41;UBERON:0000468!4.38e-15!659;UBERON:0001017!5.56e-15!82;UBERON:0001986!5.77e-15!18;UBERON:0004638!5.77e-15!18;UBERON:0004852!5.77e-15!18;UBERON:0003075!1.68e-14!86;UBERON:0007284!1.68e-14!86;UBERON:0000955!3.48e-14!69;UBERON:0006238!3.48e-14!69;UBERON:0005743!4.16e-14!86;UBERON:0002346!2.57e-13!90;UBERON:0002020!1.86e-12!34;UBERON:0003528!1.86e-12!34;UBERON:0001893!2.70e-12!34;UBERON:0002791!6.68e-12!33;UBERON:0000487!1.02e-11!22;UBERON:0000073!1.68e-11!94;UBERON:0001016!1.68e-11!94;UBERON:0001869!1.73e-11!32;UBERON:0002619!6.94e-11!22;UBERON:0000475!2.88e-10!365;UBERON:0006914!5.69e-10!25;UBERON:0000481!5.74e-10!347;UBERON:0001950!6.23e-10!20;UBERON:0004872!1.24e-09!84;UBERON:0000055!1.62e-09!69;UBERON:0000922!3.47e-09!612;UBERON:0000064!3.70e-09!219;UBERON:0000062!4.75e-09!511;UBERON:0002050!5.46e-09!605;UBERON:0005423!5.46e-09!605;UBERON:0000153!6.25e-09!129;UBERON:0007811!6.25e-09!129;UBERON:0003056!6.85e-09!61;UBERON:0000923!1.13e-08!604;UBERON:0005291!1.13e-08!604;UBERON:0006598!1.13e-08!604;UBERON:0002532!1.13e-08!604;UBERON:0000956!1.33e-08!25;UBERON:0000203!1.33e-08!25;UBERON:0004121!2.04e-08!169;UBERON:0003103!2.19e-08!69;UBERON:0000033!6.15e-08!123;UBERON:0000924!6.51e-08!173;UBERON:0006601!6.51e-08!173;UBERON:0003915!8.45e-08!9;UBERON:0004700!8.45e-08!9;UBERON:0001917!8.45e-08!9;UBERON:0002465!9.76e-08!10;UBERON:0002049!1.37e-07!79;UBERON:0007798!1.37e-07!79;UBERON:0003914!5.40e-07!118
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}}
}}

Revision as of 13:06, 5 September 2012


Full id: C1346_Endothelial_Renal_Hepatic_Lymphatic_heart_breast_adipose



Phase1 CAGE Peaks

Hg19::chr11:62344721..62344758,-p2@TUT1
Hg19::chr12:120687909..120687930,-p13@PXN
Hg19::chr12:120687948..120687971,-p6@PXN
Hg19::chrX:45060073..45060131,-p1@CXorf36
Hg19::chrX:45060135..45060149,-p2@CXorf36
Hg19::chrX:45060204..45060209,-p5@CXorf36


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:0050265RNA uridylyltransferase activity0.00512186506534793
GO:0017166vinculin binding0.0128031549908582
GO:0007172signal complex assembly0.0273045536036868



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
adult organism1.94e-45115
anatomical conduit3.29e-27241
anatomical cluster4.94e-24286
tube9.26e-21194
neural tube9.10e-2057
neural rod9.10e-2057
future spinal cord9.10e-2057
neural keel9.10e-2057
cell layer2.64e-17312
epithelium3.88e-17309
anterior neural tube5.27e-1642
regional part of brain9.04e-1659
anatomical system1.56e-15625
anatomical group2.34e-15626
regional part of forebrain2.64e-1541
forebrain2.64e-1541
future forebrain2.64e-1541
multi-cellular organism4.38e-15659
central nervous system5.56e-1582
endothelium5.77e-1518
blood vessel endothelium5.77e-1518
cardiovascular system endothelium5.77e-1518
neural plate1.68e-1486
presumptive neural plate1.68e-1486
brain3.48e-1469
future brain3.48e-1469
neurectoderm2.57e-1390
gray matter1.86e-1234
brain grey matter1.86e-1234
telencephalon2.70e-1234
regional part of telencephalon6.68e-1233
simple squamous epithelium1.02e-1122
regional part of nervous system1.68e-1194
nervous system1.68e-1194
cerebral hemisphere1.73e-1132
regional part of cerebral cortex6.94e-1122
organism subdivision2.88e-10365
squamous epithelium5.69e-1025
multi-tissue structure5.74e-10347
neocortex6.23e-1020
splanchnic layer of lateral plate mesoderm1.24e-0984
vessel1.62e-0969
embryo3.47e-09612
organ part3.70e-09219
organ4.75e-09511
embryonic structure5.46e-09605
developing anatomical structure5.46e-09605
anterior region of body6.25e-09129
craniocervical region6.25e-09129
pre-chordal neural plate6.85e-0961
germ layer1.13e-08604
embryonic tissue1.13e-08604
presumptive structure1.13e-08604
epiblast (generic)1.13e-08604
cerebral cortex1.33e-0825
pallium1.33e-0825
ectoderm-derived structure2.04e-08169
compound organ2.19e-0869
head6.15e-08123
ectoderm6.51e-08173
presumptive ectoderm6.51e-08173
endothelial tube8.45e-089
arterial system endothelium8.45e-089
endothelium of artery8.45e-089
lymphoid system9.76e-0810
vasculature1.37e-0779
vascular system1.37e-0779
epithelial tube5.40e-07118


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
GATA2#262436.3724658667770.008058821308742550.0318845034914484



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.