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Coexpression cluster:C1971: Difference between revisions

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|full_id=C1971_spleen_Endothelial_heart_lung_adipose_mature_locus
|full_id=C1971_spleen_Endothelial_heart_lung_adipose_mature_locus
|id=C1971
|id=C1971
|ontology_enrichment_celltype=CL:0002139!2.13e-24!24;CL:0000115!3.49e-22!35;CL:0000071!3.72e-18!18;CL:0002546!3.72e-18!18;CL:0002078!1.99e-15!44;CL:0000213!1.13e-09!57;CL:0000215!1.13e-09!57;CL:1000413!1.27e-09!9;CL:0005020!8.25e-08!6;CL:0002138!8.25e-08!6;CL:0005022!8.25e-08!6;CL:0002543!2.17e-07!6;CL:0002544!5.50e-07!6
|ontology_enrichment_celltype=CL:0002139!5.84e-29!24;CL:0000115!8.55e-22!36;CL:0000071!1.18e-20!18;CL:0002546!1.18e-20!18;CL:0002078!9.91e-16!45;CL:0000213!1.96e-10!58;CL:0000215!1.96e-10!58;CL:0005020!5.97e-10!6;CL:0002138!5.97e-10!6;CL:0005022!5.97e-10!6;CL:1000413!1.29e-09!9;CL:0002543!5.56e-09!6
|ontology_enrichment_disease=
|ontology_enrichment_disease=
|ontology_enrichment_uberon=UBERON:0007023!6.61e-72!115;UBERON:0001049!1.24e-38!57;UBERON:0005068!1.24e-38!57;UBERON:0006241!1.24e-38!57;UBERON:0007135!1.24e-38!57;UBERON:0002616!2.98e-31!59;UBERON:0003080!4.38e-31!42;UBERON:0002780!2.74e-30!41;UBERON:0001890!2.74e-30!41;UBERON:0006240!2.74e-30!41;UBERON:0004111!1.73e-27!241;UBERON:0000955!2.18e-27!69;UBERON:0006238!2.18e-27!69;UBERON:0003075!1.06e-26!86;UBERON:0007284!1.06e-26!86;UBERON:0001017!2.69e-26!82;UBERON:0002020!9.20e-26!34;UBERON:0003528!9.20e-26!34;UBERON:0005743!2.83e-25!86;UBERON:0000025!3.29e-25!194;UBERON:0001893!3.45e-25!34;UBERON:0002346!1.24e-24!90;UBERON:0002791!1.96e-24!33;UBERON:0001869!1.92e-23!32;UBERON:0000477!3.20e-23!286;UBERON:0000073!3.33e-22!94;UBERON:0001016!3.33e-22!94;UBERON:0002619!2.45e-20!22;UBERON:0001950!2.64e-18!20;UBERON:0003056!3.25e-18!61;UBERON:0001986!3.72e-18!18;UBERON:0004638!3.72e-18!18;UBERON:0004852!3.72e-18!18;UBERON:0000956!4.86e-17!25;UBERON:0000203!4.86e-17!25;UBERON:0000153!2.02e-14!129;UBERON:0007811!2.02e-14!129;UBERON:0000487!1.15e-13!22;UBERON:0000033!3.56e-13!123;UBERON:0000483!3.69e-13!309;UBERON:0000119!9.56e-13!312;UBERON:0000467!9.67e-13!625;UBERON:0000480!1.22e-12!626;UBERON:0000468!3.06e-12!659;UBERON:0006914!2.81e-11!25;UBERON:0004121!6.64e-11!169;UBERON:0002308!1.76e-10!9;UBERON:0000125!1.76e-10!9;UBERON:0002420!2.72e-10!9;UBERON:0007245!2.72e-10!9;UBERON:0010009!2.72e-10!9;UBERON:0010011!2.72e-10!9;UBERON:0000454!2.72e-10!9;UBERON:0000924!3.13e-10!173;UBERON:0006601!3.13e-10!173;UBERON:0003915!1.27e-09!9;UBERON:0004700!1.27e-09!9;UBERON:0001917!1.27e-09!9;UBERON:0000922!3.77e-09!612;UBERON:0002298!4.00e-09!8;UBERON:0000062!5.41e-09!511;UBERON:0002050!6.27e-09!605;UBERON:0005423!6.27e-09!605;UBERON:0003076!1.03e-08!15;UBERON:0003057!1.03e-08!15;UBERON:0000923!1.36e-08!604;UBERON:0005291!1.36e-08!604;UBERON:0006598!1.36e-08!604;UBERON:0002532!1.36e-08!604;UBERON:0001871!1.46e-08!7;UBERON:0009663!2.53e-08!7;UBERON:0000055!2.59e-08!69;UBERON:0000064!1.02e-07!219;UBERON:0001638!2.37e-07!9;UBERON:0003920!2.37e-07!9;UBERON:0004582!2.37e-07!9;UBERON:0004732!5.88e-07!13;UBERON:0000200!6.12e-07!6
|ontology_enrichment_uberon=UBERON:0007023!1.95e-69!114;UBERON:0001049!4.31e-39!56;UBERON:0005068!4.31e-39!56;UBERON:0006241!4.31e-39!56;UBERON:0007135!4.31e-39!56;UBERON:0000073!7.28e-36!53;UBERON:0002616!7.28e-36!53;UBERON:0002780!8.42e-33!41;UBERON:0001890!8.42e-33!41;UBERON:0003080!8.42e-33!41;UBERON:0006240!8.42e-33!41;UBERON:0003528!2.53e-30!34;UBERON:0002020!2.53e-30!34;UBERON:0001893!8.37e-30!34;UBERON:0004111!3.96e-28!240;UBERON:0003075!5.06e-28!82;UBERON:0007284!5.06e-28!82;UBERON:0002791!1.05e-27!32;UBERON:0001869!2.26e-27!32;UBERON:0000025!3.58e-26!192;UBERON:0002346!5.25e-26!86;UBERON:0000955!6.45e-26!68;UBERON:0006238!6.45e-26!68;UBERON:0001017!8.84e-25!81;UBERON:0002619!1.62e-22!22;UBERON:0000477!1.35e-21!373;UBERON:0001016!6.52e-21!89;UBERON:0004638!1.18e-20!18;UBERON:0001986!1.18e-20!18;UBERON:0004852!1.18e-20!18;UBERON:0010371!5.41e-20!104;UBERON:0001950!6.56e-20!20;UBERON:0003056!1.19e-19!61;UBERON:0000956!3.86e-19!25;UBERON:0000203!3.86e-19!25;UBERON:0010314!9.71e-19!132;UBERON:0000487!6.58e-16!22;UBERON:0006914!2.28e-13!25;UBERON:0000125!3.16e-13!9;UBERON:0002308!3.16e-13!9;UBERON:0002420!3.30e-13!9;UBERON:0007245!3.30e-13!9;UBERON:0010009!3.30e-13!9;UBERON:0010011!3.30e-13!9;UBERON:0000454!3.30e-13!9;UBERON:0000483!4.26e-13!306;UBERON:0000119!9.51e-13!309;UBERON:0011216!7.03e-12!223;UBERON:0009663!1.49e-10!7;UBERON:0000055!5.26e-10!68;UBERON:0004121!8.29e-10!171;UBERON:0000924!8.29e-10!171;UBERON:0006601!8.29e-10!171;UBERON:0000468!8.64e-10!656;UBERON:0001871!9.00e-10!6;UBERON:0003915!1.29e-09!9;UBERON:0004700!1.29e-09!9;UBERON:0001917!1.29e-09!9;UBERON:0000467!2.12e-09!624;UBERON:0000480!2.49e-09!625;UBERON:0000200!6.32e-09!6;UBERON:0002298!7.40e-09!6;UBERON:0002465!1.01e-08!10;UBERON:0000064!2.44e-08!218;UBERON:0000349!5.34e-08!5;UBERON:0003076!8.88e-08!15;UBERON:0003057!8.88e-08!15;UBERON:0002049!1.00e-07!78;UBERON:0007798!1.00e-07!78;UBERON:0000481!1.19e-07!342;UBERON:0001638!1.40e-07!9;UBERON:0003920!1.40e-07!9;UBERON:0004582!1.40e-07!9;UBERON:0001473!3.65e-07!8;UBERON:0004536!3.65e-07!8;UBERON:0006558!3.65e-07!8;UBERON:0002050!7.09e-07!564;UBERON:0000923!9.82e-07!560;UBERON:0010316!9.82e-07!560;UBERON:0005291!9.82e-07!560;UBERON:0006598!9.82e-07!560;UBERON:0010317!9.82e-07!560;UBERON:0002532!9.82e-07!560
|tf_chipseq_enrich=FOS#2353;5:8.9979553088944:1.69470025615156e-05:0.000389766130923173!GATA2#2624;5:12.744931733554:2.9719152914525e-06:0.000101366381817116!JUN#3725;5:12.5128291923363:3.25800591331781e-06:0.000109268747456968!MAX#4149;5:6.45255550900712:8.93743970843928e-05:0.00130785661441739
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}}
}}

Revision as of 11:54, 19 October 2012


Full id: C1971_spleen_Endothelial_heart_lung_adipose_mature_locus



Phase1 CAGE Peaks

Hg19::chr6:151004729..151004751,+p7@PLEKHG1
Hg19::chr6:151004757..151004770,+p12@PLEKHG1
Hg19::chr6:151004774..151004794,+p4@PLEKHG1
Hg19::chr6:151004802..151004822,+p3@PLEKHG1
Hg19::chr6:151004835..151004845,+p15@PLEKHG1


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
adult organism1.95e-69114
neural tube4.31e-3956
neural rod4.31e-3956
future spinal cord4.31e-3956
neural keel4.31e-3956
regional part of nervous system7.28e-3653
regional part of brain7.28e-3653
regional part of forebrain8.42e-3341
forebrain8.42e-3341
anterior neural tube8.42e-3341
future forebrain8.42e-3341
brain grey matter2.53e-3034
gray matter2.53e-3034
telencephalon8.37e-3034
anatomical conduit3.96e-28240
neural plate5.06e-2882
presumptive neural plate5.06e-2882
regional part of telencephalon1.05e-2732
cerebral hemisphere2.26e-2732
tube3.58e-26192
neurectoderm5.25e-2686
brain6.45e-2668
future brain6.45e-2668
central nervous system8.84e-2581
regional part of cerebral cortex1.62e-2222
anatomical cluster1.35e-21373
nervous system6.52e-2189
blood vessel endothelium1.18e-2018
endothelium1.18e-2018
cardiovascular system endothelium1.18e-2018
ecto-epithelium5.41e-20104
neocortex6.56e-2020
pre-chordal neural plate1.19e-1961
cerebral cortex3.86e-1925
pallium3.86e-1925
structure with developmental contribution from neural crest9.71e-19132
simple squamous epithelium6.58e-1622
squamous epithelium2.28e-1325
neural nucleus3.16e-139
nucleus of brain3.16e-139
basal ganglion3.30e-139
nuclear complex of neuraxis3.30e-139
aggregate regional part of brain3.30e-139
collection of basal ganglia3.30e-139
cerebral subcortex3.30e-139
epithelium4.26e-13306
cell layer9.51e-13309
organ system subdivision7.03e-12223
telencephalic nucleus1.49e-107
vessel5.26e-1068
ectoderm-derived structure8.29e-10171
ectoderm8.29e-10171
presumptive ectoderm8.29e-10171
multi-cellular organism8.64e-10656
temporal lobe9.00e-106
endothelial tube1.29e-099
arterial system endothelium1.29e-099
endothelium of artery1.29e-099
anatomical system2.12e-09624
anatomical group2.49e-09625
gyrus6.32e-096
brainstem7.40e-096
lymphoid system1.01e-0810
organ part2.44e-08218
limbic system5.34e-085
posterior neural tube8.88e-0815
chordal neural plate8.88e-0815
vasculature1.00e-0778
vascular system1.00e-0778
multi-tissue structure1.19e-07342
vein1.40e-079
venous blood vessel1.40e-079
venous system1.40e-079
lymphatic vessel3.65e-078
lymph vasculature3.65e-078
lymphatic part of lymphoid system3.65e-078
embryonic structure7.09e-07564
germ layer9.82e-07560
germ layer / neural crest9.82e-07560
embryonic tissue9.82e-07560
presumptive structure9.82e-07560
germ layer / neural crest derived structure9.82e-07560
epiblast (generic)9.82e-07560


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
FOS#235358.99795530889441.69470025615156e-050.000389766130923173
GATA2#2624512.7449317335542.9719152914525e-060.000101366381817116
JUN#3725512.51282919233633.25800591331781e-060.000109268747456968
MAX#414956.452555509007128.93743970843928e-050.00130785661441739



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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