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Coexpression cluster:C4831: Difference between revisions

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|full_id=C4831_smooth_aorta_optic_granulosa_colon_globus_substantia
|full_id=C4831_smooth_aorta_optic_granulosa_colon_globus_substantia
|id=C4831
|id=C4831
|ontology_enrichment_celltype=CL:0000055!7.67e-13!180
|ontology_enrichment_celltype=
|ontology_enrichment_disease=
|ontology_enrichment_disease=
|ontology_enrichment_uberon=UBERON:0007023!8.31e-35!115;UBERON:0001049!5.17e-25!57;UBERON:0005068!5.17e-25!57;UBERON:0006241!5.17e-25!57;UBERON:0007135!5.17e-25!57;UBERON:0002616!2.10e-22!59;UBERON:0001017!2.95e-22!82;UBERON:0005743!3.45e-21!86;UBERON:0003075!9.60e-21!86;UBERON:0007284!9.60e-21!86;UBERON:0000955!3.27e-20!69;UBERON:0006238!3.27e-20!69;UBERON:0000073!6.05e-20!94;UBERON:0001016!6.05e-20!94;UBERON:0003080!3.33e-19!42;UBERON:0002780!7.32e-19!41;UBERON:0001890!7.32e-19!41;UBERON:0006240!7.32e-19!41;UBERON:0002346!1.47e-18!90;UBERON:0004121!3.16e-18!169;UBERON:0000475!5.98e-17!365;UBERON:0000924!6.65e-17!173;UBERON:0006601!6.65e-17!173;UBERON:0000033!2.37e-15!123;UBERON:0002020!3.24e-15!34;UBERON:0003528!3.24e-15!34;UBERON:0001893!4.76e-15!34;UBERON:0000153!7.80e-15!129;UBERON:0007811!7.80e-15!129;UBERON:0002791!1.48e-14!33;UBERON:0003056!2.96e-14!61;UBERON:0001869!9.08e-14!32;UBERON:0000481!8.89e-11!347;UBERON:0000468!1.45e-10!659;UBERON:0000956!2.83e-10!25;UBERON:0000203!2.83e-10!25;UBERON:0002619!3.84e-10!22;UBERON:0000062!1.47e-09!511;UBERON:0001950!3.70e-09!20;UBERON:0000064!4.82e-09!219;UBERON:0000483!1.17e-08!309;UBERON:0000119!3.07e-08!312;UBERON:0000467!6.21e-08!625;UBERON:0000480!9.16e-08!626;UBERON:0000477!3.63e-07!286;UBERON:0003076!5.17e-07!15;UBERON:0003057!5.17e-07!15;UBERON:0000922!7.07e-07!612
|ontology_enrichment_uberon=UBERON:0007023!6.23e-35!114;UBERON:0001049!7.35e-26!56;UBERON:0005068!7.35e-26!56;UBERON:0006241!7.35e-26!56;UBERON:0007135!7.35e-26!56;UBERON:0000073!8.70e-24!53;UBERON:0002616!8.70e-24!53;UBERON:0001017!8.52e-22!81;UBERON:0000955!1.48e-21!68;UBERON:0006238!1.48e-21!68;UBERON:0002780!1.50e-20!41;UBERON:0001890!1.50e-20!41;UBERON:0003080!1.50e-20!41;UBERON:0006240!1.50e-20!41;UBERON:0003075!1.78e-20!82;UBERON:0007284!1.78e-20!82;UBERON:0001016!3.01e-20!89;UBERON:0010314!1.13e-19!132;UBERON:0002346!2.63e-18!86;UBERON:0010371!4.76e-17!104;UBERON:0001893!3.10e-16!34;UBERON:0003528!3.42e-16!34;UBERON:0002020!3.42e-16!34;UBERON:0003056!3.84e-15!61;UBERON:0002791!7.69e-15!32;UBERON:0001869!9.28e-15!32;UBERON:0004121!1.07e-14!171;UBERON:0000924!1.07e-14!171;UBERON:0006601!1.07e-14!171;UBERON:0000956!5.59e-11!25;UBERON:0000203!5.59e-11!25;UBERON:0002619!1.15e-10!22;UBERON:0011216!1.21e-10!223;UBERON:0001950!1.26e-09!20;UBERON:0000481!1.17e-08!342;UBERON:0000062!3.80e-08!503;UBERON:0000468!1.16e-07!656;UBERON:0000064!4.25e-07!218;UBERON:0000125!6.95e-07!9;UBERON:0002308!6.95e-07!9
|tf_chipseq_enrich=CTCF#10664;3:5.36025637307503:0.006492509252767:0.0281789957133247!E2F1#1869;3:4.90738921487932:0.00846098534723939:0.0328265109655015!EGR1#1958;3:4.98817909481014:0.00805648813738344:0.0322936697209821!MYC#4609;3:5.2222818716094:0.00702084375574015:0.0296502183989384!REST#5978;3:9.65002871612802:0.00111263624711459:0.0077211041204253!SIN3A#25942;3:5.40888472681514:0.00631896197799152:0.0278634608410157!SRF#6722;3:13.7971782621678:0.000380661502580019:0.00376761814518144!SUZ12#23512;3:50.1157809110629:7.93834897779404e-06:0.000223952790084233!TAF7#6879;3:11.4330694049239:0.000669018198194583:0.00546341321457847!USF1#7391;3:6.36149927720796:0.0038840405729056:0.0191387267465765!USF2#7392;3:12.9921973850696:0.000455897939342781:0.00423457176156357!ZNF263#10127;3:8.22184163701068:0.00179904392556587:0.0110290178763897
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}}
}}

Revision as of 16:16, 19 October 2012


Full id: C4831_smooth_aorta_optic_granulosa_colon_globus_substantia



Phase1 CAGE Peaks

Hg19::chr9:79520989..79521001,-p3@PRUNE2
Hg19::chr9:79521006..79521040,-p1@PRUNE2
Hg19::chr9:79521045..79521056,-p4@PRUNE2


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><br>uberon_data<br><br>


Uber Anatomy
Ontology termp-valuen
adult organism6.23e-35114
neural tube7.35e-2656
neural rod7.35e-2656
future spinal cord7.35e-2656
neural keel7.35e-2656
regional part of nervous system8.70e-2453
regional part of brain8.70e-2453
central nervous system8.52e-2281
brain1.48e-2168
future brain1.48e-2168
regional part of forebrain1.50e-2041
forebrain1.50e-2041
anterior neural tube1.50e-2041
future forebrain1.50e-2041
neural plate1.78e-2082
presumptive neural plate1.78e-2082
nervous system3.01e-2089
structure with developmental contribution from neural crest1.13e-19132
neurectoderm2.63e-1886
ecto-epithelium4.76e-17104
telencephalon3.10e-1634
brain grey matter3.42e-1634
gray matter3.42e-1634
pre-chordal neural plate3.84e-1561
regional part of telencephalon7.69e-1532
cerebral hemisphere9.28e-1532
ectoderm-derived structure1.07e-14171
ectoderm1.07e-14171
presumptive ectoderm1.07e-14171
cerebral cortex5.59e-1125
pallium5.59e-1125
regional part of cerebral cortex1.15e-1022
organ system subdivision1.21e-10223
neocortex1.26e-0920
multi-tissue structure1.17e-08342
organ3.80e-08503
multi-cellular organism1.16e-07656
organ part4.25e-07218
neural nucleus6.95e-079
nucleus of brain6.95e-079


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
CTCF#1066435.360256373075030.0064925092527670.0281789957133247
E2F1#186934.907389214879320.008460985347239390.0328265109655015
EGR1#195834.988179094810140.008056488137383440.0322936697209821
MYC#460935.22228187160940.007020843755740150.0296502183989384
REST#597839.650028716128020.001112636247114590.0077211041204253
SIN3A#2594235.408884726815140.006318961977991520.0278634608410157
SRF#6722313.79717826216780.0003806615025800190.00376761814518144
SUZ12#23512350.11578091106297.93834897779404e-060.000223952790084233
TAF7#6879311.43306940492390.0006690181981945830.00546341321457847
USF1#739136.361499277207960.00388404057290560.0191387267465765
USF2#7392312.99219738506960.0004558979393427810.00423457176156357
ZNF263#1012738.221841637010680.001799043925565870.0110290178763897



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.