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Coexpression cluster:C3442: Difference between revisions

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|ontology_enrichment_disease=
|ontology_enrichment_disease=
|ontology_enrichment_uberon=UBERON:0005743!6.22e-48!86;UBERON:0001017!1.88e-47!82;UBERON:0001049!1.57e-46!57;UBERON:0005068!1.57e-46!57;UBERON:0006241!1.57e-46!57;UBERON:0007135!1.57e-46!57;UBERON:0000073!3.87e-46!94;UBERON:0001016!3.87e-46!94;UBERON:0000955!4.96e-40!69;UBERON:0006238!4.96e-40!69;UBERON:0003080!3.64e-39!42;UBERON:0002780!3.28e-38!41;UBERON:0001890!3.28e-38!41;UBERON:0006240!3.28e-38!41;UBERON:0002616!4.85e-38!59;UBERON:0001869!1.30e-33!32;UBERON:0001893!2.31e-33!34;UBERON:0002020!2.95e-33!34;UBERON:0003528!2.95e-33!34;UBERON:0003075!3.43e-33!86;UBERON:0007284!3.43e-33!86;UBERON:0002346!2.80e-32!90;UBERON:0002791!5.07e-32!33;UBERON:0007023!2.56e-30!115;UBERON:0000956!3.48e-28!25;UBERON:0000203!3.48e-28!25;UBERON:0002619!5.74e-28!22;UBERON:0003056!3.32e-27!61;UBERON:0001950!6.76e-26!20;UBERON:0004121!2.24e-25!169;UBERON:0000924!3.51e-25!173;UBERON:0006601!3.51e-25!173;UBERON:0000033!5.42e-23!123;UBERON:0000153!8.91e-23!129;UBERON:0007811!8.91e-23!129;UBERON:0001737!5.43e-12!9;UBERON:0000064!2.78e-10!219;UBERON:0000200!1.44e-09!6;UBERON:0000025!1.90e-09!194;UBERON:0003076!8.07e-09!15;UBERON:0003057!8.07e-09!15;UBERON:0001871!9.44e-09!7;UBERON:0002021!1.76e-08!5;UBERON:0001872!4.43e-08!5;UBERON:0002298!4.52e-08!8;UBERON:0000922!1.09e-07!612;UBERON:0001557!2.43e-07!19;UBERON:0000477!3.52e-07!286;UBERON:0000349!4.26e-07!5;UBERON:0002308!7.71e-07!9;UBERON:0000125!7.71e-07!9;UBERON:0002420!8.63e-07!9;UBERON:0007245!8.63e-07!9;UBERON:0010009!8.63e-07!9;UBERON:0010011!8.63e-07!9;UBERON:0000454!8.63e-07!9;UBERON:0000062!9.92e-07!511
|ontology_enrichment_uberon=UBERON:0005743!6.22e-48!86;UBERON:0001017!1.88e-47!82;UBERON:0001049!1.57e-46!57;UBERON:0005068!1.57e-46!57;UBERON:0006241!1.57e-46!57;UBERON:0007135!1.57e-46!57;UBERON:0000073!3.87e-46!94;UBERON:0001016!3.87e-46!94;UBERON:0000955!4.96e-40!69;UBERON:0006238!4.96e-40!69;UBERON:0003080!3.64e-39!42;UBERON:0002780!3.28e-38!41;UBERON:0001890!3.28e-38!41;UBERON:0006240!3.28e-38!41;UBERON:0002616!4.85e-38!59;UBERON:0001869!1.30e-33!32;UBERON:0001893!2.31e-33!34;UBERON:0002020!2.95e-33!34;UBERON:0003528!2.95e-33!34;UBERON:0003075!3.43e-33!86;UBERON:0007284!3.43e-33!86;UBERON:0002346!2.80e-32!90;UBERON:0002791!5.07e-32!33;UBERON:0007023!2.56e-30!115;UBERON:0000956!3.48e-28!25;UBERON:0000203!3.48e-28!25;UBERON:0002619!5.74e-28!22;UBERON:0003056!3.32e-27!61;UBERON:0001950!6.76e-26!20;UBERON:0004121!2.24e-25!169;UBERON:0000924!3.51e-25!173;UBERON:0006601!3.51e-25!173;UBERON:0000033!5.42e-23!123;UBERON:0000153!8.91e-23!129;UBERON:0007811!8.91e-23!129;UBERON:0001737!5.43e-12!9;UBERON:0000064!2.78e-10!219;UBERON:0000200!1.44e-09!6;UBERON:0000025!1.90e-09!194;UBERON:0003076!8.07e-09!15;UBERON:0003057!8.07e-09!15;UBERON:0001871!9.44e-09!7;UBERON:0002021!1.76e-08!5;UBERON:0001872!4.43e-08!5;UBERON:0002298!4.52e-08!8;UBERON:0000922!1.09e-07!612;UBERON:0001557!2.43e-07!19;UBERON:0000477!3.52e-07!286;UBERON:0000349!4.26e-07!5;UBERON:0002308!7.71e-07!9;UBERON:0000125!7.71e-07!9;UBERON:0002420!8.63e-07!9;UBERON:0007245!8.63e-07!9;UBERON:0010009!8.63e-07!9;UBERON:0010011!8.63e-07!9;UBERON:0000454!8.63e-07!9;UBERON:0000062!9.92e-07!511
|tf_chipseq_enrich=CTCF#10664;3:5.36025637307503:0.006492509252767:0.0278892433615651!REST#5978;3:9.65002871612802:0.00111263624711459:0.00766356374150238
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}}
}}

Revision as of 13:15, 5 September 2012


Full id: C3442_amniotic_epitheloid_occipital_brain_retina_frontal_medial



Phase1 CAGE Peaks

Hg19::chr14:63512137..63512153,-p2@KCNH5
Hg19::chr14:63512154..63512187,-p1@KCNH5
Hg19::chr14:63512678..63512708,-p@chr14:63512678..63512708
-


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 system1.88e-4782
neural tube1.57e-4657
neural rod1.57e-4657
future spinal cord1.57e-4657
neural keel1.57e-4657
regional part of nervous system3.87e-4694
nervous system3.87e-4694
brain4.96e-4069
future brain4.96e-4069
anterior neural tube3.64e-3942
regional part of forebrain3.28e-3841
forebrain3.28e-3841
future forebrain3.28e-3841
regional part of brain4.85e-3859
cerebral hemisphere1.30e-3332
telencephalon2.31e-3334
gray matter2.95e-3334
brain grey matter2.95e-3334
neural plate3.43e-3386
presumptive neural plate3.43e-3386
neurectoderm2.80e-3290
regional part of telencephalon5.07e-3233
adult organism2.56e-30115
cerebral cortex3.48e-2825
pallium3.48e-2825
regional part of cerebral cortex5.74e-2822
pre-chordal neural plate3.32e-2761
neocortex6.76e-2620
ectoderm-derived structure2.24e-25169
ectoderm3.51e-25173
presumptive ectoderm3.51e-25173
head5.42e-23123
anterior region of body8.91e-23129
craniocervical region8.91e-23129
larynx5.43e-129
organ part2.78e-10219
gyrus1.44e-096
tube1.90e-09194
posterior neural tube8.07e-0915
chordal neural plate8.07e-0915
temporal lobe9.44e-097
occipital lobe1.76e-085
parietal lobe4.43e-085
brainstem4.52e-088
embryo1.09e-07612
upper respiratory tract2.43e-0719
anatomical cluster3.52e-07286
limbic system4.26e-075
nucleus of brain7.71e-079
neural nucleus7.71e-079
basal ganglion8.63e-079
nuclear complex of neuraxis8.63e-079
aggregate regional part of brain8.63e-079
collection of basal ganglia8.63e-079
cerebral subcortex8.63e-079
organ9.92e-07511


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#1066435.360256373075030.0064925092527670.0278892433615651
REST#597839.650028716128020.001112636247114590.00766356374150238



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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