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Coexpression cluster:C3715: Difference between revisions

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|ontology_enrichment_celltype=
|ontology_enrichment_celltype=
|ontology_enrichment_disease=
|ontology_enrichment_disease=
|ontology_enrichment_uberon=UBERON:0001049!6.01e-23!57;UBERON:0005068!6.01e-23!57;UBERON:0006241!6.01e-23!57;UBERON:0007135!6.01e-23!57;UBERON:0005743!1.07e-22!86;UBERON:0000955!1.59e-22!69;UBERON:0006238!1.59e-22!69;UBERON:0003075!1.88e-22!86;UBERON:0007284!1.88e-22!86;UBERON:0001017!5.14e-22!82;UBERON:0002616!3.64e-21!59;UBERON:0000073!1.18e-20!94;UBERON:0001016!1.18e-20!94;UBERON:0002780!1.18e-19!41;UBERON:0001890!1.18e-19!41;UBERON:0006240!1.18e-19!41;UBERON:0003080!1.82e-19!42;UBERON:0002346!2.24e-19!90;UBERON:0000483!1.18e-17!309;UBERON:0003056!1.75e-17!61;UBERON:0000119!1.91e-17!312;UBERON:0000025!9.49e-17!194;UBERON:0001869!1.29e-16!32;UBERON:0002020!2.42e-16!34;UBERON:0003528!2.42e-16!34;UBERON:0001893!2.43e-16!34;UBERON:0000033!3.60e-16!123;UBERON:0002791!1.12e-15!33;UBERON:0000153!1.32e-15!129;UBERON:0007811!1.32e-15!129;UBERON:0004121!2.44e-15!169;UBERON:0004111!3.79e-15!241;UBERON:0000477!1.01e-14!286;UBERON:0007023!1.78e-14!115;UBERON:0000924!1.11e-13!173;UBERON:0006601!1.11e-13!173;UBERON:0002619!1.74e-13!22;UBERON:0000956!2.27e-13!25;UBERON:0000203!2.27e-13!25;UBERON:0001950!2.63e-12!20;UBERON:0000475!7.38e-11!365;UBERON:0000481!5.62e-10!347;UBERON:0000064!8.96e-10!219
|ontology_enrichment_uberon=UBERON:0001049!4.20e-24!56;UBERON:0005068!4.20e-24!56;UBERON:0006241!4.20e-24!56;UBERON:0007135!4.20e-24!56;UBERON:0000073!1.43e-23!53;UBERON:0002616!1.43e-23!53;UBERON:0000955!3.35e-23!68;UBERON:0006238!3.35e-23!68;UBERON:0001017!6.00e-23!81;UBERON:0002780!1.38e-20!41;UBERON:0001890!1.38e-20!41;UBERON:0003080!1.38e-20!41;UBERON:0006240!1.38e-20!41;UBERON:0001016!3.02e-20!89;UBERON:0003075!2.65e-19!82;UBERON:0007284!2.65e-19!82;UBERON:0010371!1.36e-17!104;UBERON:0001869!2.35e-17!32;UBERON:0001893!3.13e-17!34;UBERON:0003528!3.40e-17!34;UBERON:0002020!3.40e-17!34;UBERON:0003056!2.10e-16!61;UBERON:0002346!2.31e-16!86;UBERON:0002791!3.47e-16!32;UBERON:0000025!1.52e-15!192;UBERON:0010314!1.83e-15!132;UBERON:0002619!3.34e-14!22;UBERON:0007023!3.57e-14!114;UBERON:0000956!5.16e-14!25;UBERON:0000203!5.16e-14!25;UBERON:0004111!8.19e-14!240;UBERON:0000119!3.98e-13!309;UBERON:0000483!5.11e-13!306;UBERON:0001950!5.25e-13!20;UBERON:0000477!1.87e-12!373;UBERON:0004121!1.21e-11!171;UBERON:0000924!1.21e-11!171;UBERON:0006601!1.21e-11!171;UBERON:0011216!1.87e-09!223;UBERON:0000481!3.38e-08!342;UBERON:0000064!4.27e-08!218
|tf_chipseq_enrich=CTCF#10664;3:5.36025637307503:0.006492509252767:0.0279271488405986!E2F1#1869;3:4.90738921487932:0.00846098534723939:0.0325112895025877!E2F6#1876;3:5.01715573169739:0.0079176980688633:0.0321957821450714!EBF1#1879;3:8.906466846569:0.0014152328356098:0.00914694610546769!EGR1#1958;3:4.98817909481014:0.00805648813738344:0.0320464489861437!ELF1#1997;3:4.25809795880754:0.0129517987505461:0.0461962675355447!GABPB1#2553;3:7.06768383618217:0.00283221282541742:0.0154018992592434!NFKB1#4790;3:5.48806342419384:0.00604938181565543:0.0269455106173599!PAX5#5079;3:6.66956553117783:0.00337029099967726:0.0172823597837332!SRF#6722;3:13.7971782621678:0.000380661502580019:0.00374878893615791!TAF7#6879;3:11.4330694049239:0.000669018198194583:0.0054252342263564!YY1#7528;3:4.91117074985386:0.00844145534180826:0.0329145848214715
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}}
}}

Revision as of 15:20, 19 October 2012


Full id: C3715_occipital_paracentral_medial_amygdala_postcentral_parietal_brain



Phase1 CAGE Peaks

Hg19::chr18:29265234..29265252,-p@chr18:29265234..29265252
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Hg19::chr18:29265256..29265304,-p@chr18:29265256..29265304
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Hg19::chr18:29265316..29265333,-p@chr18:29265316..29265333
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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
neural tube4.20e-2456
neural rod4.20e-2456
future spinal cord4.20e-2456
neural keel4.20e-2456
regional part of nervous system1.43e-2353
regional part of brain1.43e-2353
brain3.35e-2368
future brain3.35e-2368
central nervous system6.00e-2381
regional part of forebrain1.38e-2041
forebrain1.38e-2041
anterior neural tube1.38e-2041
future forebrain1.38e-2041
nervous system3.02e-2089
neural plate2.65e-1982
presumptive neural plate2.65e-1982
ecto-epithelium1.36e-17104
cerebral hemisphere2.35e-1732
telencephalon3.13e-1734
brain grey matter3.40e-1734
gray matter3.40e-1734
pre-chordal neural plate2.10e-1661
neurectoderm2.31e-1686
regional part of telencephalon3.47e-1632
tube1.52e-15192
structure with developmental contribution from neural crest1.83e-15132
regional part of cerebral cortex3.34e-1422
adult organism3.57e-14114
cerebral cortex5.16e-1425
pallium5.16e-1425
anatomical conduit8.19e-14240
cell layer3.98e-13309
epithelium5.11e-13306
neocortex5.25e-1320
anatomical cluster1.87e-12373
ectoderm-derived structure1.21e-11171
ectoderm1.21e-11171
presumptive ectoderm1.21e-11171
organ system subdivision1.87e-09223
multi-tissue structure3.38e-08342
organ part4.27e-08218


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#1066435.360256373075030.0064925092527670.0279271488405986
E2F1#186934.907389214879320.008460985347239390.0325112895025877
E2F6#187635.017155731697390.00791769806886330.0321957821450714
EBF1#187938.9064668465690.00141523283560980.00914694610546769
EGR1#195834.988179094810140.008056488137383440.0320464489861437
ELF1#199734.258097958807540.01295179875054610.0461962675355447
GABPB1#255337.067683836182170.002832212825417420.0154018992592434
NFKB1#479035.488063424193840.006049381815655430.0269455106173599
PAX5#507936.669565531177830.003370290999677260.0172823597837332
SRF#6722313.79717826216780.0003806615025800190.00374878893615791
TAF7#6879311.43306940492390.0006690181981945830.0054252342263564
YY1#752834.911170749853860.008441455341808260.0329145848214715



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.