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Coexpression cluster:C3067: Difference between revisions

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|ontology_enrichment_celltype=
|ontology_enrichment_celltype=
|ontology_enrichment_disease=
|ontology_enrichment_disease=
|ontology_enrichment_uberon=UBERON:0000481!5.83e-22!347;UBERON:0007023!1.99e-19!115;UBERON:0001017!3.43e-19!82;UBERON:0005743!1.35e-18!86;UBERON:0000073!2.69e-17!94;UBERON:0001016!2.69e-17!94;UBERON:0000955!2.10e-16!69;UBERON:0006238!2.10e-16!69;UBERON:0000477!4.48e-15!286;UBERON:0001049!3.78e-14!57;UBERON:0005068!3.78e-14!57;UBERON:0006241!3.78e-14!57;UBERON:0007135!3.78e-14!57;UBERON:0002616!4.06e-14!59;UBERON:0000475!1.07e-13!365;UBERON:0000119!1.23e-13!312;UBERON:0000483!1.76e-13!309;UBERON:0000153!2.39e-13!129;UBERON:0007811!2.39e-13!129;UBERON:0000033!4.95e-13!123;UBERON:0004111!5.52e-13!241;UBERON:0003075!6.78e-13!86;UBERON:0007284!6.78e-13!86;UBERON:0000025!3.10e-12!194;UBERON:0004121!3.38e-12!169;UBERON:0000468!1.36e-11!659;UBERON:0000922!1.38e-11!612;UBERON:0000062!3.45e-11!511;UBERON:0003080!3.50e-11!42;UBERON:0002346!3.82e-11!90;UBERON:0000924!4.96e-11!173;UBERON:0006601!4.96e-11!173;UBERON:0002780!1.05e-10!41;UBERON:0001890!1.05e-10!41;UBERON:0006240!1.05e-10!41;UBERON:0000467!3.09e-10!625;UBERON:0000480!5.88e-10!626;UBERON:0003056!2.82e-09!61;UBERON:0002050!3.56e-09!605;UBERON:0005423!3.56e-09!605;UBERON:0000923!7.46e-09!604;UBERON:0005291!7.46e-09!604;UBERON:0006598!7.46e-09!604;UBERON:0002532!7.46e-09!604;UBERON:0002020!8.91e-09!34;UBERON:0003528!8.91e-09!34;UBERON:0001893!1.10e-08!34;UBERON:0002791!1.34e-08!33;UBERON:0001869!4.44e-08!32;UBERON:0003104!4.45e-08!238;UBERON:0009142!4.45e-08!238;UBERON:0000064!9.93e-08!219;UBERON:0001007!3.52e-07!155;UBERON:0001555!3.52e-07!155;UBERON:0007026!3.52e-07!155
|ontology_enrichment_uberon=UBERON:0000477!2.41e-28!373;UBERON:0011216!3.52e-27!223;UBERON:0000481!1.07e-26!342;UBERON:0001017!8.10e-20!81;UBERON:0001016!1.16e-18!89;UBERON:0007023!1.87e-18!114;UBERON:0000955!7.61e-17!68;UBERON:0006238!7.61e-17!68;UBERON:0001049!9.98e-15!56;UBERON:0005068!9.98e-15!56;UBERON:0006241!9.98e-15!56;UBERON:0007135!9.98e-15!56;UBERON:0000119!1.99e-14!309;UBERON:0000483!4.39e-14!306;UBERON:0003075!7.26e-14!82;UBERON:0007284!7.26e-14!82;UBERON:0000073!2.44e-13!53;UBERON:0002616!2.44e-13!53;UBERON:0004111!3.31e-13!240;UBERON:0000025!2.15e-12!192;UBERON:0002346!5.34e-12!86;UBERON:0010314!6.32e-12!132;UBERON:0000468!1.12e-11!656;UBERON:0004121!1.27e-11!171;UBERON:0000924!1.27e-11!171;UBERON:0006601!1.27e-11!171;UBERON:0002780!1.44e-11!41;UBERON:0001890!1.44e-11!41;UBERON:0003080!1.44e-11!41;UBERON:0006240!1.44e-11!41;UBERON:0000922!2.46e-11!592;UBERON:0000062!1.51e-10!503;UBERON:0000467!2.44e-10!624;UBERON:0010371!3.09e-10!104;UBERON:0003056!4.12e-10!61;UBERON:0000480!4.53e-10!625;UBERON:0003104!1.85e-09!160;UBERON:0009142!1.85e-09!160;UBERON:0003528!2.11e-09!34;UBERON:0002020!2.11e-09!34;UBERON:0005423!2.65e-09!581;UBERON:0001893!2.73e-09!34;UBERON:0001007!4.59e-09!145;UBERON:0001555!4.59e-09!145;UBERON:0007026!4.59e-09!145;UBERON:0002791!8.10e-09!32;UBERON:0005409!1.07e-08!25;UBERON:0001869!1.22e-08!32;UBERON:0004921!4.36e-08!118;UBERON:0000064!8.70e-08!218;UBERON:0004119!1.50e-07!160;UBERON:0000925!1.50e-07!160;UBERON:0006595!1.50e-07!160;UBERON:0002050!3.05e-07!564;UBERON:0000956!3.64e-07!25;UBERON:0000203!3.64e-07!25;UBERON:0005172!4.59e-07!54;UBERON:0005173!4.59e-07!54;UBERON:0003929!5.12e-07!54;UBERON:0000160!5.54e-07!17
|tf_chipseq_enrich=E2F1#1869;3:4.90738921487932:0.00846098534723939:0.0323541611262571!EGR1#1958;3:4.98817909481014:0.00805648813738344:0.0319030698635091!ELF1#1997;3:4.25809795880754:0.0129517987505461:0.0460030237283459!GABPB1#2553;3:7.06768383618217:0.00283221282541742:0.0153635005076492!MEF2A#4205;3:18.7432309096441:0.000151824390562247:0.00194748065904329!SIN3A#25942;3:5.40888472681514:0.00631896197799152:0.027536763332198!TCF12#6938;3:10.6344649021864:0.000831352399020207:0.00627624788212168
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}}
}}

Revision as of 14:46, 19 October 2012


Full id: C3067_medulloblastoma_lung_placenta_renal_retina_gall_rectum



Phase1 CAGE Peaks

Hg19::chr11:100557931..100557947,+p4@ARHGAP42
Hg19::chr11:100557958..100558008,+p2@ARHGAP42
Hg19::chr11:100558010..100558029,+p1@ARHGAP42


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
anatomical cluster2.41e-28373
organ system subdivision3.52e-27223
multi-tissue structure1.07e-26342
central nervous system8.10e-2081
nervous system1.16e-1889
adult organism1.87e-18114
brain7.61e-1768
future brain7.61e-1768
neural tube9.98e-1556
neural rod9.98e-1556
future spinal cord9.98e-1556
neural keel9.98e-1556
cell layer1.99e-14309
epithelium4.39e-14306
neural plate7.26e-1482
presumptive neural plate7.26e-1482
regional part of nervous system2.44e-1353
regional part of brain2.44e-1353
anatomical conduit3.31e-13240
tube2.15e-12192
neurectoderm5.34e-1286
structure with developmental contribution from neural crest6.32e-12132
multi-cellular organism1.12e-11656
ectoderm-derived structure1.27e-11171
ectoderm1.27e-11171
presumptive ectoderm1.27e-11171
regional part of forebrain1.44e-1141
forebrain1.44e-1141
anterior neural tube1.44e-1141
future forebrain1.44e-1141
embryo2.46e-11592
organ1.51e-10503
anatomical system2.44e-10624
ecto-epithelium3.09e-10104
pre-chordal neural plate4.12e-1061
anatomical group4.53e-10625
mesenchyme1.85e-09160
entire embryonic mesenchyme1.85e-09160
brain grey matter2.11e-0934
gray matter2.11e-0934
developing anatomical structure2.65e-09581
telencephalon2.73e-0934
digestive system4.59e-09145
digestive tract4.59e-09145
primitive gut4.59e-09145
regional part of telencephalon8.10e-0932
gastrointestinal system1.07e-0825
cerebral hemisphere1.22e-0832
subdivision of digestive tract4.36e-08118
organ part8.70e-08218
endoderm-derived structure1.50e-07160
endoderm1.50e-07160
presumptive endoderm1.50e-07160
embryonic structure3.05e-07564
cerebral cortex3.64e-0725
pallium3.64e-0725
abdomen element4.59e-0754
abdominal segment element4.59e-0754
gut epithelium5.12e-0754
intestine5.54e-0717


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
E2F1#186934.907389214879320.008460985347239390.0323541611262571
EGR1#195834.988179094810140.008056488137383440.0319030698635091
ELF1#199734.258097958807540.01295179875054610.0460030237283459
GABPB1#255337.067683836182170.002832212825417420.0153635005076492
MEF2A#4205318.74323090964410.0001518243905622470.00194748065904329
SIN3A#2594235.408884726815140.006318961977991520.027536763332198
TCF12#6938310.63446490218640.0008313523990202070.00627624788212168



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.

Retrieved from "http://f5-webapp4.gsc.riken.jp/resource_browser/index.php?title=Coexpression_cluster:C3067&oldid=2249252"