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Coexpression cluster:C2776: Difference between revisions

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|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: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
|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 14:18, 5 September 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
central nervous system8.39e-4182
neural tube1.21e-3957
neural rod1.21e-3957
future spinal cord1.21e-3957
neural keel1.21e-3957
cerebral hemisphere4.69e-3832
telencephalon2.46e-3734
gray matter2.72e-3734
brain grey matter2.72e-3734
brain7.05e-3769
future brain7.05e-3769
regional part of forebrain5.14e-3641
forebrain5.14e-3641
future forebrain5.14e-3641
regional part of telencephalon5.78e-3633
regional part of nervous system9.54e-3694
nervous system9.54e-3694
anterior neural tube7.04e-3542
neurectoderm3.55e-3490
regional part of brain4.40e-3459
neural plate1.38e-3186
presumptive neural plate1.38e-3186
cerebral cortex9.52e-2925
pallium9.52e-2925
neocortex1.14e-2820
regional part of cerebral cortex3.82e-2822
pre-chordal neural plate1.36e-2761
head3.20e-24123
anterior region of body1.69e-23129
craniocervical region1.69e-23129
ectoderm3.32e-22173
presumptive ectoderm3.32e-22173
ectoderm-derived structure3.01e-20169
adult organism3.96e-15115
larynx4.46e-159
temporal lobe1.50e-117
basal ganglion3.93e-109
nuclear complex of neuraxis3.93e-109
aggregate regional part of brain3.93e-109
collection of basal ganglia3.93e-109
cerebral subcortex3.93e-109
nucleus of brain6.68e-109
neural nucleus6.68e-109
gyrus7.19e-106
anatomical cluster5.77e-09286
upper respiratory tract1.63e-0819
parietal lobe3.92e-085
telencephalic nucleus6.46e-087
occipital lobe6.70e-085
corpus striatum4.12e-074
striatum4.12e-074
ventral part of telencephalon4.12e-074
future corpus striatum4.12e-074


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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