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Coexpression cluster:C2776: Difference between revisions

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|ontology_enrichment_celltype=
|ontology_enrichment_celltype=
|ontology_enrichment_disease=
|ontology_enrichment_disease=
|ontology_enrichment_uberon=UBERON:0001017!8.39e-41!82;UBERON:0001049!1.21e-39!57;UBERON:0005068!1.21e-39!57;UBERON:0006241!1.21e-39!57;UBERON:0007135!1.21e-39!57;UBERON:0005743!1.70e-39!86;UBERON:0001869!4.69e-38!32;UBERON:0001893!2.46e-37!34;UBERON:0002020!2.72e-37!34;UBERON:0003528!2.72e-37!34;UBERON:0000955!7.05e-37!69;UBERON:0006238!7.05e-37!69;UBERON:0002780!5.14e-36!41;UBERON:0001890!5.14e-36!41;UBERON:0006240!5.14e-36!41;UBERON:0002791!5.78e-36!33;UBERON:0000073!9.54e-36!94;UBERON:0001016!9.54e-36!94;UBERON:0003080!7.04e-35!42;UBERON:0002346!3.55e-34!90;UBERON:0002616!4.40e-34!59;UBERON:0003075!1.38e-31!86;UBERON:0007284!1.38e-31!86;UBERON:0000956!9.52e-29!25;UBERON:0000203!9.52e-29!25;UBERON:0001950!1.14e-28!20;UBERON:0002619!3.82e-28!22;UBERON:0003056!1.36e-27!61;UBERON:0000033!3.20e-24!123;UBERON:0000153!1.69e-23!129;UBERON:0007811!1.69e-23!129;UBERON:0000924!3.32e-22!173;UBERON:0006601!3.32e-22!173;UBERON:0004121!3.01e-20!169;UBERON:0007023!3.96e-15!115;UBERON:0001737!4.46e-15!9;UBERON:0001871!1.50e-11!7;UBERON:0002420!3.93e-10!9;UBERON:0007245!3.93e-10!9;UBERON:0010009!3.93e-10!9;UBERON:0010011!3.93e-10!9;UBERON:0000454!3.93e-10!9;UBERON:0002308!6.68e-10!9;UBERON:0000125!6.68e-10!9;UBERON:0000200!7.19e-10!6;UBERON:0000477!5.77e-09!286;UBERON:0001557!1.63e-08!19;UBERON:0001872!3.92e-08!5;UBERON:0009663!6.46e-08!7;UBERON:0002021!6.70e-08!5;UBERON:0000369!4.12e-07!4;UBERON:0002435!4.12e-07!4;UBERON:0000204!4.12e-07!4;UBERON:0010082!4.12e-07!4
|ontology_enrichment_uberon=UBERON:0001869!1.21e-50!32;UBERON:0001893!1.98e-50!34;UBERON:0003528!4.36e-50!34;UBERON:0002020!4.36e-50!34;UBERON:0002780!1.20e-49!41;UBERON:0001890!1.20e-49!41;UBERON:0003080!1.20e-49!41;UBERON:0006240!1.20e-49!41;UBERON:0000073!6.16e-49!53;UBERON:0002616!6.16e-49!53;UBERON:0000955!7.71e-47!68;UBERON:0006238!7.71e-47!68;UBERON:0002791!8.35e-47!32;UBERON:0001049!9.33e-46!56;UBERON:0005068!9.33e-46!56;UBERON:0006241!9.33e-46!56;UBERON:0007135!9.33e-46!56;UBERON:0001017!8.54e-42!81;UBERON:0003056!7.74e-39!61;UBERON:0002346!9.41e-39!86;UBERON:0001016!1.44e-38!89;UBERON:0000956!1.22e-36!25;UBERON:0000203!1.22e-36!25;UBERON:0001950!4.75e-35!20;UBERON:0003075!6.26e-35!82;UBERON:0007284!6.26e-35!82;UBERON:0002619!6.68e-35!22;UBERON:0010371!4.32e-25!104;UBERON:0004121!1.95e-23!171;UBERON:0000924!1.95e-23!171;UBERON:0006601!1.95e-23!171;UBERON:0001737!3.26e-22!9;UBERON:0011216!3.64e-22!223;UBERON:0010314!7.11e-21!132;UBERON:0007023!2.33e-15!114;UBERON:0000125!1.19e-14!9;UBERON:0002308!1.19e-14!9;UBERON:0000200!3.80e-14!6;UBERON:0000064!2.37e-12!218;UBERON:0001557!1.08e-11!19;UBERON:0001872!1.24e-11!5;UBERON:0002420!1.66e-11!9;UBERON:0007245!1.66e-11!9;UBERON:0010009!1.66e-11!9;UBERON:0010011!1.66e-11!9;UBERON:0000454!1.66e-11!9;UBERON:0009663!1.71e-11!7;UBERON:0002021!3.21e-11!5;UBERON:0000477!6.20e-11!373;UBERON:0000369!6.32e-10!4;UBERON:0002435!6.32e-10!4;UBERON:0000204!6.32e-10!4;UBERON:0010082!6.32e-10!4;UBERON:0000481!5.30e-09!342;UBERON:0001870!3.94e-08!3;UBERON:0002298!4.81e-08!6;UBERON:0001871!6.80e-08!6;UBERON:0005383!8.07e-08!3;UBERON:0005382!8.07e-08!3;UBERON:0000025!5.52e-07!192
|tf_chipseq_enrich=CTCF#10664;4:5.36025637307503:0.00121114538164362:0.00819081865657439!GATA2#2624;4:12.744931733554:3.78864877853583e-05:0.000723633302453372!RAD21#5885;4:10.3550338954563:8.6948481184721e-05:0.00129762966939855!SMC3#9126;4:15.0449328449328:1.95092670935632e-05:0.00043912248835876
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}}
}}

Revision as of 14:24, 19 October 2012


Full id: C2776_NK_Hep2_plasma_medial_neuroblastoma_caudate_frontal



Phase1 CAGE Peaks

Hg19::chr4:134076051..134076081,+p3@PCDH10
Hg19::chr4:134076088..134076099,+p5@PCDH10
Hg19::chr4:134076101..134076115,+p9@PCDH10
Hg19::chr4:134076121..134076131,+p15@PCDH10


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
cerebral hemisphere1.21e-5032
telencephalon1.98e-5034
brain grey matter4.36e-5034
gray matter4.36e-5034
regional part of forebrain1.20e-4941
forebrain1.20e-4941
anterior neural tube1.20e-4941
future forebrain1.20e-4941
regional part of nervous system6.16e-4953
regional part of brain6.16e-4953
brain7.71e-4768
future brain7.71e-4768
regional part of telencephalon8.35e-4732
neural tube9.33e-4656
neural rod9.33e-4656
future spinal cord9.33e-4656
neural keel9.33e-4656
central nervous system8.54e-4281
pre-chordal neural plate7.74e-3961
neurectoderm9.41e-3986
nervous system1.44e-3889
cerebral cortex1.22e-3625
pallium1.22e-3625
neocortex4.75e-3520
neural plate6.26e-3582
presumptive neural plate6.26e-3582
regional part of cerebral cortex6.68e-3522
ecto-epithelium4.32e-25104
ectoderm-derived structure1.95e-23171
ectoderm1.95e-23171
presumptive ectoderm1.95e-23171
larynx3.26e-229
organ system subdivision3.64e-22223
structure with developmental contribution from neural crest7.11e-21132
adult organism2.33e-15114
neural nucleus1.19e-149
nucleus of brain1.19e-149
gyrus3.80e-146
organ part2.37e-12218
upper respiratory tract1.08e-1119
parietal lobe1.24e-115
basal ganglion1.66e-119
nuclear complex of neuraxis1.66e-119
aggregate regional part of brain1.66e-119
collection of basal ganglia1.66e-119
cerebral subcortex1.66e-119
telencephalic nucleus1.71e-117
occipital lobe3.21e-115
anatomical cluster6.20e-11373
corpus striatum6.32e-104
striatum6.32e-104
ventral part of telencephalon6.32e-104
future corpus striatum6.32e-104
multi-tissue structure5.30e-09342
frontal cortex3.94e-083
brainstem4.81e-086
temporal lobe6.80e-086
caudate-putamen8.07e-083
dorsal striatum8.07e-083
tube5.52e-07192


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#1066445.360256373075030.001211145381643620.00819081865657439
GATA2#2624412.7449317335543.78864877853583e-050.000723633302453372
RAD21#5885410.35503389545638.6948481184721e-050.00129762966939855
SMC3#9126415.04493284493281.95092670935632e-050.00043912248835876



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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