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Coexpression cluster:C428: Difference between revisions

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|gostat_on_coexpression_clusters=GO:0019899!enzyme binding!0.0128383398671892!7450;25780;5074$GO:0005515!protein binding!0.0185725221551354!5787;5074;4281;947;2078;375449;7450;25780$GO:0033093!Weibel-Palade body!0.0196043800777111!7450$GO:0031091!platelet alpha granule!0.0294031075667311!7450$GO:0046582!Rap GTPase activator activity!0.0352795745910804!25780$GO:0002020!protease binding!0.0391949118586822!7450$GO:0001948!glycoprotein binding!0.0499485389194682!7450$GO:0043687!post-translational protein modification!0.0499485389194682!5787;375449;2078;4281
|gostat_on_coexpression_clusters=GO:0019899!enzyme binding!0.0128383398671892!7450;25780;5074$GO:0005515!protein binding!0.0185725221551354!5787;5074;4281;947;2078;375449;7450;25780$GO:0033093!Weibel-Palade body!0.0196043800777111!7450$GO:0031091!platelet alpha granule!0.0294031075667311!7450$GO:0046582!Rap GTPase activator activity!0.0352795745910804!25780$GO:0002020!protease binding!0.0391949118586822!7450$GO:0001948!glycoprotein binding!0.0499485389194682!7450$GO:0043687!post-translational protein modification!0.0499485389194682!5787;375449;2078;4281
|id=C428
|id=C428
|ontology_enrichment_celltype=CL:0002139!3.69e-17!24;CL:0000115!5.42e-15!35;CL:0000071!3.85e-13!18;CL:0002546!3.85e-13!18;CL:0002078!1.35e-09!44;CL:0000213!1.91e-07!57;CL:0000215!1.91e-07!57;CL:1000413!2.55e-07!9
|ontology_enrichment_disease=
|ontology_enrichment_uberon=UBERON:0007023!3.29e-43!115;UBERON:0004111!7.02e-20!241;UBERON:0000025!3.94e-18!194;UBERON:0001009!3.18e-16!113;UBERON:0000477!4.39e-16!286;UBERON:0001049!1.43e-15!57;UBERON:0005068!1.43e-15!57;UBERON:0006241!1.43e-15!57;UBERON:0007135!1.43e-15!57;UBERON:0004535!6.07e-15!110;UBERON:0000055!9.54e-15!69;UBERON:0001986!3.85e-13!18;UBERON:0004638!3.85e-13!18;UBERON:0004852!3.85e-13!18;UBERON:0004872!9.15e-13!84;UBERON:0002616!1.00e-12!59;UBERON:0003080!2.13e-12!42;UBERON:0002049!2.64e-12!79;UBERON:0007798!2.64e-12!79;UBERON:0001981!2.65e-12!60;UBERON:0007500!2.65e-12!60;UBERON:0004537!2.65e-12!60;UBERON:0006965!2.65e-12!60;UBERON:0003075!2.73e-12!86;UBERON:0007284!2.73e-12!86;UBERON:0002780!7.19e-12!41;UBERON:0001890!7.19e-12!41;UBERON:0006240!7.19e-12!41;UBERON:0002346!9.77e-11!90;UBERON:0000955!3.31e-10!69;UBERON:0006238!3.31e-10!69;UBERON:0001017!5.44e-10!82;UBERON:0005743!7.47e-10!86;UBERON:0002020!7.68e-10!34;UBERON:0003528!7.68e-10!34;UBERON:0001893!1.04e-09!34;UBERON:0003081!1.08e-09!216;UBERON:0000487!1.21e-09!22;UBERON:0002791!2.13e-09!33;UBERON:0001869!5.50e-09!32;UBERON:0002619!1.21e-08!22;UBERON:0003056!3.63e-08!61;UBERON:0001950!6.06e-08!20;UBERON:0000483!1.09e-07!309;UBERON:0000153!1.15e-07!129;UBERON:0007811!1.15e-07!129;UBERON:0003914!1.22e-07!118;UBERON:0000073!1.35e-07!94;UBERON:0001016!1.35e-07!94;UBERON:0000119!1.77e-07!312;UBERON:0006914!1.88e-07!25;UBERON:0003915!2.55e-07!9;UBERON:0004700!2.55e-07!9;UBERON:0001917!2.55e-07!9;UBERON:0000033!7.13e-07!123
}}
}}

Revision as of 14:46, 21 May 2012


Full id: C428_Endothelial_Renal_Lymphatic_Hepatic_adipose_heart_breast



Phase1 CAGE Peaks

Hg19::chr10:13908291..13908320,-p@chr10:13908291..13908320
-
Hg19::chr12:6233727..6233738,-p5@VWF
Hg19::chr12:6233757..6233771,-p4@VWF
Hg19::chr12:6233828..6233843,-p1@VWF
Hg19::chr12:6234045..6234103,-p6@VWF
Hg19::chr12:71031185..71031215,-p1@PTPRB
Hg19::chr12:71031220..71031229,-p10@PTPRB
Hg19::chr12:71031247..71031262,-p7@PTPRB
Hg19::chr12:80084018..80084035,-p17@PAWR
Hg19::chr16:75285224..75285236,-p@chr16:75285224..75285236
-
Hg19::chr1:208063620..208063634,-p4@CD34
Hg19::chr21:39870339..39870443,-p1@ERG
Hg19::chr21:39875765..39875785,+p@chr21:39875765..39875785
+
Hg19::chr2:225266743..225266773,-p1@FAM124B
Hg19::chr2:225266813..225266830,-p2@FAM124B
Hg19::chr2:33661382..33661445,+p3@RASGRP3
Hg19::chr4:56814149..56814167,-p@chr4:56814149..56814167
-
Hg19::chr4:56814168..56814203,-p@chr4:56814168..56814203
-
Hg19::chr5:61874637..61874685,+p1@LRRC70
p2@IPO11
Hg19::chr5:66124590..66124644,+p2@MAST4
Hg19::chr7:11871574..11871633,-p3@THSD7A
Hg19::chr9:139538920..139538940,-p@chr9:139538920..139538940
-
Hg19::chrX:10544942..10544977,-p5@MID1


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:0019899enzyme binding0.0128383398671892
GO:0005515protein binding0.0185725221551354
GO:0033093Weibel-Palade body0.0196043800777111
GO:0031091platelet alpha granule0.0294031075667311
GO:0046582Rap GTPase activator activity0.0352795745910804
GO:0002020protease binding0.0391949118586822
GO:0001948glycoprotein binding0.0499485389194682
GO:0043687post-translational protein modification0.0499485389194682



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 organism3.29e-43115
anatomical conduit7.02e-20241
tube3.94e-18194
circulatory system3.18e-16113
anatomical cluster4.39e-16286
neural tube1.43e-1557
neural rod1.43e-1557
future spinal cord1.43e-1557
neural keel1.43e-1557
cardiovascular system6.07e-15110
vessel9.54e-1569
endothelium3.85e-1318
blood vessel endothelium3.85e-1318
cardiovascular system endothelium3.85e-1318
splanchnic layer of lateral plate mesoderm9.15e-1384
regional part of brain1.00e-1259
anterior neural tube2.13e-1242
vasculature2.64e-1279
vascular system2.64e-1279
blood vessel2.65e-1260
epithelial tube open at both ends2.65e-1260
blood vasculature2.65e-1260
vascular cord2.65e-1260
neural plate2.73e-1286
presumptive neural plate2.73e-1286
regional part of forebrain7.19e-1241
forebrain7.19e-1241
future forebrain7.19e-1241
neurectoderm9.77e-1190
brain3.31e-1069
future brain3.31e-1069
central nervous system5.44e-1082
gray matter7.68e-1034
brain grey matter7.68e-1034
telencephalon1.04e-0934
lateral plate mesoderm1.08e-09216
simple squamous epithelium1.21e-0922
regional part of telencephalon2.13e-0933
cerebral hemisphere5.50e-0932
regional part of cerebral cortex1.21e-0822
pre-chordal neural plate3.63e-0861
neocortex6.06e-0820
epithelium1.09e-07309
anterior region of body1.15e-07129
craniocervical region1.15e-07129
epithelial tube1.22e-07118
regional part of nervous system1.35e-0794
nervous system1.35e-0794
cell layer1.77e-07312
squamous epithelium1.88e-0725
endothelial tube2.55e-079
arterial system endothelium2.55e-079
endothelium of artery2.55e-079
head7.13e-07123


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


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.