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Coexpression cluster:C409: Difference between revisions

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|ontology_enrichment_disease=
|ontology_enrichment_disease=
|ontology_enrichment_uberon=UBERON:0007023!1.68e-52!115;UBERON:0001049!2.73e-19!57;UBERON:0005068!2.73e-19!57;UBERON:0006241!2.73e-19!57;UBERON:0007135!2.73e-19!57;UBERON:0002616!5.45e-19!59;UBERON:0000955!1.00e-16!69;UBERON:0006238!1.00e-16!69;UBERON:0001017!1.39e-16!82;UBERON:0005743!4.28e-16!86;UBERON:0003080!1.74e-15!42;UBERON:0004111!3.05e-15!241;UBERON:0002780!7.73e-15!41;UBERON:0001890!7.73e-15!41;UBERON:0006240!7.73e-15!41;UBERON:0003075!1.21e-14!86;UBERON:0007284!1.21e-14!86;UBERON:0000073!2.81e-14!94;UBERON:0001016!2.81e-14!94;UBERON:0000477!5.78e-14!286;UBERON:0002346!7.21e-14!90;UBERON:0000468!1.33e-13!659;UBERON:0000025!1.04e-12!194;UBERON:0002020!2.81e-12!34;UBERON:0003528!2.81e-12!34;UBERON:0001893!3.64e-12!34;UBERON:0002791!8.40e-12!33;UBERON:0000480!1.44e-11!626;UBERON:0000467!1.93e-11!625;UBERON:0000153!1.99e-11!129;UBERON:0007811!1.99e-11!129;UBERON:0001869!2.61e-11!32;UBERON:0003056!6.43e-11!61;UBERON:0000033!1.83e-10!123;UBERON:0002619!9.46e-10!22;UBERON:0000119!2.29e-09!312;UBERON:0001950!5.46e-09!20;UBERON:0000922!6.16e-09!612;UBERON:0000483!6.74e-09!309;UBERON:0000956!9.99e-09!25;UBERON:0000203!9.99e-09!25;UBERON:0004121!2.31e-08!169;UBERON:0000924!4.29e-08!173;UBERON:0006601!4.29e-08!173;UBERON:0000062!6.61e-08!511;UBERON:0002050!7.83e-08!605;UBERON:0005423!7.83e-08!605;UBERON:0000923!1.35e-07!604;UBERON:0005291!1.35e-07!604;UBERON:0006598!1.35e-07!604;UBERON:0002532!1.35e-07!604;UBERON:0001009!2.25e-07!113;UBERON:0000475!7.14e-07!365;UBERON:0001986!8.62e-07!18;UBERON:0004638!8.62e-07!18;UBERON:0004852!8.62e-07!18
|ontology_enrichment_uberon=UBERON:0007023!1.68e-52!115;UBERON:0001049!2.73e-19!57;UBERON:0005068!2.73e-19!57;UBERON:0006241!2.73e-19!57;UBERON:0007135!2.73e-19!57;UBERON:0002616!5.45e-19!59;UBERON:0000955!1.00e-16!69;UBERON:0006238!1.00e-16!69;UBERON:0001017!1.39e-16!82;UBERON:0005743!4.28e-16!86;UBERON:0003080!1.74e-15!42;UBERON:0004111!3.05e-15!241;UBERON:0002780!7.73e-15!41;UBERON:0001890!7.73e-15!41;UBERON:0006240!7.73e-15!41;UBERON:0003075!1.21e-14!86;UBERON:0007284!1.21e-14!86;UBERON:0000073!2.81e-14!94;UBERON:0001016!2.81e-14!94;UBERON:0000477!5.78e-14!286;UBERON:0002346!7.21e-14!90;UBERON:0000468!1.33e-13!659;UBERON:0000025!1.04e-12!194;UBERON:0002020!2.81e-12!34;UBERON:0003528!2.81e-12!34;UBERON:0001893!3.64e-12!34;UBERON:0002791!8.40e-12!33;UBERON:0000480!1.44e-11!626;UBERON:0000467!1.93e-11!625;UBERON:0000153!1.99e-11!129;UBERON:0007811!1.99e-11!129;UBERON:0001869!2.61e-11!32;UBERON:0003056!6.43e-11!61;UBERON:0000033!1.83e-10!123;UBERON:0002619!9.46e-10!22;UBERON:0000119!2.29e-09!312;UBERON:0001950!5.46e-09!20;UBERON:0000922!6.16e-09!612;UBERON:0000483!6.74e-09!309;UBERON:0000956!9.99e-09!25;UBERON:0000203!9.99e-09!25;UBERON:0004121!2.31e-08!169;UBERON:0000924!4.29e-08!173;UBERON:0006601!4.29e-08!173;UBERON:0000062!6.61e-08!511;UBERON:0002050!7.83e-08!605;UBERON:0005423!7.83e-08!605;UBERON:0000923!1.35e-07!604;UBERON:0005291!1.35e-07!604;UBERON:0006598!1.35e-07!604;UBERON:0002532!1.35e-07!604;UBERON:0001009!2.25e-07!113;UBERON:0000475!7.14e-07!365;UBERON:0001986!8.62e-07!18;UBERON:0004638!8.62e-07!18;UBERON:0004852!8.62e-07!18
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}}
}}

Revision as of 19:43, 8 August 2012


Full id: C409_adipose_mature_breast_lung_skeletal_Melanocyte_left



Phase1 CAGE Peaks

Hg19::chr10:45472158..45472178,-p@chr10:45472158..45472178
-
Hg19::chr10:45472831..45472842,-p@chr10:45472831..45472842
-
Hg19::chr10:45472893..45472939,-p@chr10:45472893..45472939
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Hg19::chr10:45472995..45473006,-p3@C10orf10
Hg19::chr10:45473374..45473404,-p2@C10orf10
Hg19::chr12:109554288..109554295,+p24@ACACB
Hg19::chr12:12938586..12938600,+p1@APOLD1
Hg19::chr12:76646060..76646067,+p@chr12:76646060..76646067
+
Hg19::chr12:798987..798990,+p@chr12:798987..798990
+
Hg19::chr13:40951436..40951448,-p@chr13:40951436..40951448
-
Hg19::chr17:41924511..41924520,+p2@CD300LG
Hg19::chr17:41924536..41924550,+p1@CD300LG
Hg19::chr17:41926073..41926086,+p@chr17:41926073..41926086
+
Hg19::chr17:62038824..62038843,-p@chr17:62038824..62038843
-
Hg19::chr1:101616154..101616184,+p@chr1:101616154..101616184
+
Hg19::chr3:12189970..12189984,+p4@SYN2
Hg19::chr3:153271174..153271192,-p@chr3:153271174..153271192
-
Hg19::chr3:179457862..179457876,+p@chr3:179457862..179457876
+
Hg19::chr4:190708714..190708723,-p@chr4:190708714..190708723
-
Hg19::chr5:157942095..157942109,-p@chr5:157942095..157942109
-
Hg19::chr5:180257481..180257485,+p3@ENST00000501855
Hg19::chr5:180467219..180467244,+p3@BTNL9
Hg19::chr5:180467259..180467278,+p1@BTNL9
Hg19::chr5:180467283..180467299,+p4@BTNL9
Hg19::chr7:80154162..80154173,+p@chr7:80154162..80154173
+


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:0003989acetyl-CoA carboxylase activity0.0286075869072858
GO:0004075biotin carboxylase activity0.0286075869072858
GO:0016421CoA carboxylase activity0.0333656946030637
GO:0016885ligase activity, forming carbon-carbon bonds0.0333656946030637



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 organism1.68e-52115
neural tube2.73e-1957
neural rod2.73e-1957
future spinal cord2.73e-1957
neural keel2.73e-1957
regional part of brain5.45e-1959
brain1.00e-1669
future brain1.00e-1669
central nervous system1.39e-1682
anterior neural tube1.74e-1542
anatomical conduit3.05e-15241
regional part of forebrain7.73e-1541
forebrain7.73e-1541
future forebrain7.73e-1541
neural plate1.21e-1486
presumptive neural plate1.21e-1486
regional part of nervous system2.81e-1494
nervous system2.81e-1494
anatomical cluster5.78e-14286
neurectoderm7.21e-1490
multi-cellular organism1.33e-13659
tube1.04e-12194
gray matter2.81e-1234
brain grey matter2.81e-1234
telencephalon3.64e-1234
regional part of telencephalon8.40e-1233
anatomical group1.44e-11626
anatomical system1.93e-11625
anterior region of body1.99e-11129
craniocervical region1.99e-11129
cerebral hemisphere2.61e-1132
pre-chordal neural plate6.43e-1161
head1.83e-10123
regional part of cerebral cortex9.46e-1022
cell layer2.29e-09312
neocortex5.46e-0920
embryo6.16e-09612
epithelium6.74e-09309
cerebral cortex9.99e-0925
pallium9.99e-0925
ectoderm-derived structure2.31e-08169
ectoderm4.29e-08173
presumptive ectoderm4.29e-08173
organ6.61e-08511
embryonic structure7.83e-08605
developing anatomical structure7.83e-08605
germ layer1.35e-07604
embryonic tissue1.35e-07604
presumptive structure1.35e-07604
epiblast (generic)1.35e-07604
circulatory system2.25e-07113
organism subdivision7.14e-07365
endothelium8.62e-0718
blood vessel endothelium8.62e-0718
cardiovascular system endothelium8.62e-0718


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)

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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.