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Coexpression cluster:C1887: Difference between revisions

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|gostat_on_coexpression_clusters=GO:0017034!Rap guanyl-nucleotide exchange factor activity!0.00565162999117592!9771$GO:0030742!GTP-dependent protein binding!0.015539923662318!9771
|gostat_on_coexpression_clusters=GO:0017034!Rap guanyl-nucleotide exchange factor activity!0.00565162999117592!9771$GO:0030742!GTP-dependent protein binding!0.015539923662318!9771
|id=C1887
|id=C1887
|ontology_enrichment_celltype=CL:0002139!5.63e-22!24;CL:0000115!9.68e-19!35;CL:0000071!2.47e-16!18;CL:0002546!2.47e-16!18;CL:0002078!2.84e-13!44;CL:1000413!9.02e-09!9;CL:0000213!2.06e-08!57;CL:0000215!2.06e-08!57;CL:0005020!3.25e-07!6;CL:0002138!3.25e-07!6;CL:0005022!3.25e-07!6;CL:0000222!5.11e-07!119
|ontology_enrichment_celltype=CL:0002139!1.93e-28!24;CL:0000115!2.73e-25!36;CL:0000071!5.34e-21!18;CL:0002546!5.34e-21!18;CL:0002078!3.96e-18!45;CL:0000213!6.93e-12!58;CL:0000215!6.93e-12!58;CL:1000413!2.67e-11!9;CL:0005020!5.21e-09!6;CL:0002138!5.21e-09!6;CL:0005022!5.21e-09!6;CL:0002543!5.53e-08!6;CL:0002544!8.34e-08!6
|ontology_enrichment_disease=
|ontology_enrichment_disease=
|ontology_enrichment_uberon=UBERON:0007023!1.99e-53!115;UBERON:0004111!6.44e-40!241;UBERON:0000025!1.69e-37!194;UBERON:0000477!3.62e-36!286;UBERON:0004872!9.36e-25!84;UBERON:0000055!2.30e-24!69;UBERON:0000483!7.79e-23!309;UBERON:0000119!3.63e-22!312;UBERON:0001049!3.32e-21!57;UBERON:0005068!3.32e-21!57;UBERON:0006241!3.32e-21!57;UBERON:0007135!3.32e-21!57;UBERON:0002049!6.29e-21!79;UBERON:0007798!6.29e-21!79;UBERON:0001981!1.94e-20!60;UBERON:0007500!1.94e-20!60;UBERON:0004537!1.94e-20!60;UBERON:0006965!1.94e-20!60;UBERON:0003914!4.23e-20!118;UBERON:0001009!6.88e-20!113;UBERON:0004535!3.03e-18!110;UBERON:0002616!4.12e-17!59;UBERON:0003080!1.99e-16!42;UBERON:0001986!2.47e-16!18;UBERON:0004638!2.47e-16!18;UBERON:0004852!2.47e-16!18;UBERON:0003075!8.44e-16!86;UBERON:0007284!8.44e-16!86;UBERON:0002780!1.01e-15!41;UBERON:0001890!1.01e-15!41;UBERON:0006240!1.01e-15!41;UBERON:0000468!3.10e-15!659;UBERON:0000467!1.39e-14!625;UBERON:0001017!1.52e-14!82;UBERON:0000480!1.88e-14!626;UBERON:0002346!2.74e-14!90;UBERON:0005743!6.23e-14!86;UBERON:0000955!1.25e-13!69;UBERON:0006238!1.25e-13!69;UBERON:0000487!3.13e-13!22;UBERON:0000073!1.00e-12!94;UBERON:0001016!1.00e-12!94;UBERON:0002020!1.09e-12!34;UBERON:0003528!1.09e-12!34;UBERON:0001893!1.81e-12!34;UBERON:0002791!4.93e-12!33;UBERON:0006914!1.07e-11!25;UBERON:0001869!2.04e-11!32;UBERON:0000481!2.45e-11!347;UBERON:0001950!7.64e-11!20;UBERON:0001637!8.62e-11!42;UBERON:0003509!8.62e-11!42;UBERON:0004572!8.62e-11!42;UBERON:0002619!1.51e-10!22;UBERON:0000922!4.32e-10!612;UBERON:0000475!1.01e-09!365;UBERON:0003056!1.31e-09!61;UBERON:0002050!1.38e-09!605;UBERON:0005423!1.38e-09!605;UBERON:0000923!3.35e-09!604;UBERON:0005291!3.35e-09!604;UBERON:0006598!3.35e-09!604;UBERON:0002532!3.35e-09!604;UBERON:0007100!6.65e-09!27;UBERON:0003915!9.02e-09!9;UBERON:0004700!9.02e-09!9;UBERON:0001917!9.02e-09!9;UBERON:0000956!1.44e-08!25;UBERON:0000203!1.44e-08!25;UBERON:0000490!1.55e-08!138;UBERON:0003103!5.41e-08!69;UBERON:0000153!8.59e-08!129;UBERON:0007811!8.59e-08!129;UBERON:0002465!1.80e-07!10;UBERON:0004573!2.06e-07!33;UBERON:0004571!2.06e-07!33;UBERON:0000948!3.81e-07!24;UBERON:0005498!3.81e-07!24;UBERON:0004140!3.81e-07!24;UBERON:0009881!3.81e-07!24;UBERON:0004141!3.81e-07!24;UBERON:0003084!3.81e-07!24;UBERON:0007005!3.81e-07!24;UBERON:0004139!3.81e-07!24;UBERON:0004291!3.81e-07!24;UBERON:0004121!4.78e-07!169;UBERON:0000033!6.78e-07!123
|ontology_enrichment_uberon=UBERON:0007023!9.18e-55!114;UBERON:0004111!1.97e-31!240;UBERON:0000025!4.63e-28!192;UBERON:0000477!7.18e-27!373;UBERON:0004638!5.34e-21!18;UBERON:0001986!5.34e-21!18;UBERON:0004852!5.34e-21!18;UBERON:0000055!6.68e-18!68;UBERON:0001049!1.03e-16!56;UBERON:0005068!1.03e-16!56;UBERON:0006241!1.03e-16!56;UBERON:0007135!1.03e-16!56;UBERON:0000487!4.89e-16!22;UBERON:0004872!5.56e-16!83;UBERON:0000483!1.80e-15!306;UBERON:0000119!4.76e-15!309;UBERON:0000073!2.29e-14!53;UBERON:0002616!2.29e-14!53;UBERON:0007500!5.17e-14!59;UBERON:0001981!5.17e-14!59;UBERON:0004537!5.17e-14!59;UBERON:0006965!5.17e-14!59;UBERON:0002049!5.22e-14!78;UBERON:0007798!5.22e-14!78;UBERON:0003914!5.94e-14!117;UBERON:0006914!2.18e-13!25;UBERON:0003075!3.28e-13!82;UBERON:0007284!3.28e-13!82;UBERON:0001009!3.89e-13!112;UBERON:0000468!3.78e-12!656;UBERON:0002346!4.72e-12!86;UBERON:0010314!5.16e-12!132;UBERON:0002780!5.69e-12!41;UBERON:0001890!5.69e-12!41;UBERON:0003080!5.69e-12!41;UBERON:0006240!5.69e-12!41;UBERON:0004535!1.57e-11!109;UBERON:0003915!2.67e-11!9;UBERON:0004700!2.67e-11!9;UBERON:0001917!2.67e-11!9;UBERON:0001017!4.16e-11!81;UBERON:0000481!4.26e-11!342;UBERON:0000467!9.94e-11!624;UBERON:0000480!1.20e-10!625;UBERON:0003528!5.08e-10!34;UBERON:0002020!5.08e-10!34;UBERON:0011216!5.45e-10!223;UBERON:0001893!9.69e-10!34;UBERON:0001016!1.11e-09!89;UBERON:0000955!1.24e-09!68;UBERON:0006238!1.24e-09!68;UBERON:0010371!2.45e-09!104;UBERON:0002050!4.13e-09!564;UBERON:0000923!6.25e-09!560;UBERON:0010316!6.25e-09!560;UBERON:0005291!6.25e-09!560;UBERON:0006598!6.25e-09!560;UBERON:0010317!6.25e-09!560;UBERON:0002532!6.25e-09!560;UBERON:0000922!7.73e-09!592;UBERON:0005423!9.52e-09!581;UBERON:0002791!1.00e-08!32;UBERON:0001869!1.29e-08!32;UBERON:0001950!2.82e-08!20;UBERON:0002619!2.93e-08!22;UBERON:0003103!3.08e-08!68;UBERON:0002465!4.68e-08!10;UBERON:0003056!3.00e-07!61;UBERON:0000956!7.42e-07!25;UBERON:0000203!7.42e-07!25
|tf_chipseq_enrich=GATA2#2624;5:12.744931733554:2.9719152914525e-06:0.00010120112850473
|tf_chipseq_enrich=GATA2#2624;5:12.744931733554:2.9719152914525e-06:0.00010120112850473
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}}
}}

Revision as of 11:48, 19 October 2012


Full id: C1887_lung_Endothelial_adipose_heart_spleen_Hepatocyte_penis



Phase1 CAGE Peaks

Hg19::chr2:197226832..197226859,-p4@HECW2
Hg19::chr7:22259789..22259809,-p7@RAPGEF5
Hg19::chr7:22259826..22259838,-p11@RAPGEF5
Hg19::chr7:22259845..22259864,-p5@RAPGEF5
Hg19::chr7:22259867..22259876,-p13@RAPGEF5


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:0017034Rap guanyl-nucleotide exchange factor activity0.00565162999117592
GO:0030742GTP-dependent protein binding0.015539923662318



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 organism9.18e-55114
anatomical conduit1.97e-31240
tube4.63e-28192
anatomical cluster7.18e-27373
blood vessel endothelium5.34e-2118
endothelium5.34e-2118
cardiovascular system endothelium5.34e-2118
vessel6.68e-1868
neural tube1.03e-1656
neural rod1.03e-1656
future spinal cord1.03e-1656
neural keel1.03e-1656
simple squamous epithelium4.89e-1622
splanchnic layer of lateral plate mesoderm5.56e-1683
epithelium1.80e-15306
cell layer4.76e-15309
regional part of nervous system2.29e-1453
regional part of brain2.29e-1453
epithelial tube open at both ends5.17e-1459
blood vessel5.17e-1459
blood vasculature5.17e-1459
vascular cord5.17e-1459
vasculature5.22e-1478
vascular system5.22e-1478
epithelial tube5.94e-14117
squamous epithelium2.18e-1325
neural plate3.28e-1382
presumptive neural plate3.28e-1382
circulatory system3.89e-13112
multi-cellular organism3.78e-12656
neurectoderm4.72e-1286
structure with developmental contribution from neural crest5.16e-12132
regional part of forebrain5.69e-1241
forebrain5.69e-1241
anterior neural tube5.69e-1241
future forebrain5.69e-1241
cardiovascular system1.57e-11109
endothelial tube2.67e-119
arterial system endothelium2.67e-119
endothelium of artery2.67e-119
central nervous system4.16e-1181
multi-tissue structure4.26e-11342
anatomical system9.94e-11624
anatomical group1.20e-10625
brain grey matter5.08e-1034
gray matter5.08e-1034
organ system subdivision5.45e-10223
telencephalon9.69e-1034
nervous system1.11e-0989
brain1.24e-0968
future brain1.24e-0968
ecto-epithelium2.45e-09104
embryonic structure4.13e-09564
germ layer6.25e-09560
germ layer / neural crest6.25e-09560
embryonic tissue6.25e-09560
presumptive structure6.25e-09560
germ layer / neural crest derived structure6.25e-09560
epiblast (generic)6.25e-09560
embryo7.73e-09592
developing anatomical structure9.52e-09581
regional part of telencephalon1.00e-0832
cerebral hemisphere1.29e-0832
neocortex2.82e-0820
regional part of cerebral cortex2.93e-0822
compound organ3.08e-0868
lymphoid system4.68e-0810
pre-chordal neural plate3.00e-0761
cerebral cortex7.42e-0725
pallium7.42e-0725


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

(#promoters = Number of promoters in this coexpression cluster that have ChIP signal of the TF)

TF#promotersEnrichmentp-valueq-value
GATA2#2624512.7449317335542.9719152914525e-060.00010120112850473



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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