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Coexpression cluster:C4056: Difference between revisions

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|ontology_enrichment_celltype=
|ontology_enrichment_celltype=
|ontology_enrichment_disease=
|ontology_enrichment_disease=
|ontology_enrichment_uberon=UBERON:0007023!1.78e-62!115;UBERON:0001049!9.94e-46!57;UBERON:0005068!9.94e-46!57;UBERON:0006241!9.94e-46!57;UBERON:0007135!9.94e-46!57;UBERON:0002616!1.97e-37!59;UBERON:0003080!2.43e-37!42;UBERON:0001017!1.80e-36!82;UBERON:0002780!2.60e-36!41;UBERON:0001890!2.60e-36!41;UBERON:0006240!2.60e-36!41;UBERON:0005743!7.55e-36!86;UBERON:0003075!7.27e-34!86;UBERON:0007284!7.27e-34!86;UBERON:0000073!2.07e-33!94;UBERON:0001016!2.07e-33!94;UBERON:0000955!2.10e-32!69;UBERON:0006238!2.10e-32!69;UBERON:0002346!1.36e-31!90;UBERON:0003056!1.56e-28!61;UBERON:0001893!4.09e-28!34;UBERON:0002020!1.10e-27!34;UBERON:0003528!1.10e-27!34;UBERON:0002791!6.72e-27!33;UBERON:0000153!9.03e-27!129;UBERON:0007811!9.03e-27!129;UBERON:0001869!6.25e-26!32;UBERON:0000033!3.22e-25!123;UBERON:0004121!8.01e-24!169;UBERON:0000924!8.64e-23!173;UBERON:0006601!8.64e-23!173;UBERON:0002619!1.21e-21!22;UBERON:0001950!1.28e-19!20;UBERON:0000956!2.22e-18!25;UBERON:0000203!2.22e-18!25;UBERON:0000064!2.40e-12!219;UBERON:0000481!2.57e-12!347;UBERON:0000062!4.68e-12!511;UBERON:0002308!4.84e-11!9;UBERON:0000125!4.84e-11!9;UBERON:0002420!5.17e-11!9;UBERON:0007245!5.17e-11!9;UBERON:0010009!5.17e-11!9;UBERON:0010011!5.17e-11!9;UBERON:0000454!5.17e-11!9;UBERON:0002298!1.22e-10!8;UBERON:0000475!2.86e-10!365;UBERON:0000922!3.23e-10!612;UBERON:0001871!5.84e-10!7;UBERON:0001894!8.66e-10!7;UBERON:0006222!8.66e-10!7;UBERON:0003076!1.42e-09!15;UBERON:0003057!1.42e-09!15;UBERON:0002050!3.83e-09!605;UBERON:0005423!3.83e-09!605;UBERON:0009663!4.44e-09!7;UBERON:0000468!7.18e-09!659;UBERON:0000923!1.12e-08!604;UBERON:0005291!1.12e-08!604;UBERON:0006598!1.12e-08!604;UBERON:0002532!1.12e-08!604;UBERON:0000467!1.57e-08!625;UBERON:0000480!1.83e-08!626;UBERON:0000477!2.06e-08!286;UBERON:0004111!2.96e-08!241;UBERON:0000025!6.15e-08!194;UBERON:0000483!7.97e-08!309;UBERON:0000119!1.41e-07!312;UBERON:0001872!5.61e-07!5;UBERON:0000349!8.84e-07!5;UBERON:0005409!9.36e-07!35
|ontology_enrichment_uberon=UBERON:0007023!3.29e-46!114;UBERON:0001049!2.51e-29!56;UBERON:0005068!2.51e-29!56;UBERON:0006241!2.51e-29!56;UBERON:0007135!2.51e-29!56;UBERON:0000073!4.77e-27!53;UBERON:0002616!4.77e-27!53;UBERON:0003075!3.17e-23!82;UBERON:0007284!3.17e-23!82;UBERON:0002780!1.44e-22!41;UBERON:0001890!1.44e-22!41;UBERON:0003080!1.44e-22!41;UBERON:0006240!1.44e-22!41;UBERON:0002346!1.09e-21!86;UBERON:0000955!2.51e-20!68;UBERON:0006238!2.51e-20!68;UBERON:0011216!5.17e-20!223;UBERON:0001017!6.26e-20!81;UBERON:0001893!1.45e-18!34;UBERON:0003056!1.31e-17!61;UBERON:0010371!1.38e-17!104;UBERON:0001016!4.61e-17!89;UBERON:0003528!1.64e-16!34;UBERON:0002020!1.64e-16!34;UBERON:0001869!5.20e-16!32;UBERON:0002791!6.89e-16!32;UBERON:0010314!7.75e-15!132;UBERON:0000481!2.19e-14!342;UBERON:0004121!1.60e-13!171;UBERON:0000924!1.60e-13!171;UBERON:0006601!1.60e-13!171;UBERON:0002619!1.66e-12!22;UBERON:0000477!3.70e-12!373;UBERON:0001950!6.60e-12!20;UBERON:0000956!1.05e-10!25;UBERON:0000203!1.05e-10!25;UBERON:0000062!1.23e-09!503;UBERON:0002298!7.96e-09!6;UBERON:0000922!2.75e-08!592;UBERON:0000064!4.91e-08!218;UBERON:0002108!6.03e-08!4;UBERON:0003076!6.48e-08!15;UBERON:0003057!6.48e-08!15;UBERON:0005423!1.19e-07!581;UBERON:0000125!1.22e-07!9;UBERON:0002308!1.22e-07!9;UBERON:0002420!1.41e-07!9;UBERON:0007245!1.41e-07!9;UBERON:0010009!1.41e-07!9;UBERON:0010011!1.41e-07!9;UBERON:0000454!1.41e-07!9;UBERON:0004111!3.21e-07!240;UBERON:0009663!3.32e-07!7;UBERON:0000160!3.43e-07!17;UBERON:0001896!3.75e-07!3;UBERON:0005290!3.75e-07!3;UBERON:0010096!3.75e-07!3;UBERON:0005409!4.01e-07!25;UBERON:0002050!5.58e-07!564
|tf_chipseq_enrich=SUZ12#23512;3:50.1157809110629:7.93834897779404e-06:0.000222989034129056
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}}
}}

Revision as of 15:38, 19 October 2012


Full id: C4056_retina_anaplastic_pituitary_small_salivary_submaxillary_thyroid



Phase1 CAGE Peaks

Hg19::chr20:57875631..57875638,+p6@EDN3
Hg19::chr20:57875644..57875657,+p3@EDN3
Hg19::chr20:57875658..57875673,+p1@EDN3


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
adult organism3.29e-46114
neural tube2.51e-2956
neural rod2.51e-2956
future spinal cord2.51e-2956
neural keel2.51e-2956
regional part of nervous system4.77e-2753
regional part of brain4.77e-2753
neural plate3.17e-2382
presumptive neural plate3.17e-2382
regional part of forebrain1.44e-2241
forebrain1.44e-2241
anterior neural tube1.44e-2241
future forebrain1.44e-2241
neurectoderm1.09e-2186
brain2.51e-2068
future brain2.51e-2068
organ system subdivision5.17e-20223
central nervous system6.26e-2081
telencephalon1.45e-1834
pre-chordal neural plate1.31e-1761
ecto-epithelium1.38e-17104
nervous system4.61e-1789
brain grey matter1.64e-1634
gray matter1.64e-1634
cerebral hemisphere5.20e-1632
regional part of telencephalon6.89e-1632
structure with developmental contribution from neural crest7.75e-15132
multi-tissue structure2.19e-14342
ectoderm-derived structure1.60e-13171
ectoderm1.60e-13171
presumptive ectoderm1.60e-13171
regional part of cerebral cortex1.66e-1222
anatomical cluster3.70e-12373
neocortex6.60e-1220
cerebral cortex1.05e-1025
pallium1.05e-1025
organ1.23e-09503
brainstem7.96e-096
embryo2.75e-08592
organ part4.91e-08218
small intestine6.03e-084
posterior neural tube6.48e-0815
chordal neural plate6.48e-0815
developing anatomical structure1.19e-07581
neural nucleus1.22e-079
nucleus of brain1.22e-079
basal ganglion1.41e-079
nuclear complex of neuraxis1.41e-079
aggregate regional part of brain1.41e-079
collection of basal ganglia1.41e-079
cerebral subcortex1.41e-079
anatomical conduit3.21e-07240
telencephalic nucleus3.32e-077
intestine3.43e-0717
medulla oblongata3.75e-073
myelencephalon3.75e-073
future myelencephalon3.75e-073
gastrointestinal system4.01e-0725
embryonic structure5.58e-07564


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
SUZ12#23512350.11578091106297.93834897779404e-060.000222989034129056



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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