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Coexpression cluster:C3393: Difference between revisions

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|ontology_enrichment_celltype=
|ontology_enrichment_celltype=
|ontology_enrichment_disease=
|ontology_enrichment_disease=
|ontology_enrichment_uberon=UBERON:0007023!2.60e-44!115;UBERON:0001049!1.37e-41!57;UBERON:0005068!1.37e-41!57;UBERON:0006241!1.37e-41!57;UBERON:0007135!1.37e-41!57;UBERON:0003075!6.06e-41!86;UBERON:0007284!6.06e-41!86;UBERON:0005743!6.56e-41!86;UBERON:0002346!2.45e-39!90;UBERON:0000073!7.41e-38!94;UBERON:0001016!7.41e-38!94;UBERON:0001017!1.10e-37!82;UBERON:0002616!1.25e-37!59;UBERON:0000955!2.23e-35!69;UBERON:0006238!2.23e-35!69;UBERON:0003056!6.87e-34!61;UBERON:0003080!1.52e-33!42;UBERON:0002780!7.40e-33!41;UBERON:0001890!7.40e-33!41;UBERON:0006240!7.40e-33!41;UBERON:0002020!7.39e-27!34;UBERON:0003528!7.39e-27!34;UBERON:0001893!1.22e-26!34;UBERON:0002791!9.69e-26!33;UBERON:0001869!5.87e-25!32;UBERON:0000153!1.07e-23!129;UBERON:0007811!1.07e-23!129;UBERON:0000033!1.75e-23!123;UBERON:0004121!5.37e-23!169;UBERON:0000924!1.38e-22!173;UBERON:0006601!1.38e-22!173;UBERON:0002619!4.71e-22!22;UBERON:0001950!1.27e-20!20;UBERON:0000064!1.68e-18!219;UBERON:0000956!2.56e-18!25;UBERON:0000203!2.56e-18!25;UBERON:0000483!1.27e-16!309;UBERON:0000119!4.43e-16!312;UBERON:0000025!2.09e-15!194;UBERON:0000481!3.33e-15!347;UBERON:0000475!2.33e-12!365;UBERON:0000062!2.66e-11!511;UBERON:0004111!8.56e-11!241;UBERON:0002308!3.69e-10!9;UBERON:0000125!3.69e-10!9;UBERON:0000477!3.93e-10!286;UBERON:0000922!4.45e-10!612;UBERON:0002420!1.42e-09!9;UBERON:0007245!1.42e-09!9;UBERON:0010009!1.42e-09!9;UBERON:0010011!1.42e-09!9;UBERON:0000454!1.42e-09!9;UBERON:0003076!3.43e-09!15;UBERON:0003057!3.43e-09!15;UBERON:0000468!4.24e-09!659;UBERON:0002298!7.85e-09!8;UBERON:0002050!7.91e-09!605;UBERON:0005423!7.91e-09!605;UBERON:0001871!1.21e-08!7;UBERON:0000923!1.44e-08!604;UBERON:0005291!1.44e-08!604;UBERON:0006598!1.44e-08!604;UBERON:0002532!1.44e-08!604;UBERON:0009663!3.57e-08!7;UBERON:0001894!1.27e-07!7;UBERON:0006222!1.27e-07!7;UBERON:0004732!1.58e-07!13;UBERON:0000200!2.86e-07!6;UBERON:0000063!5.25e-07!97
|ontology_enrichment_uberon=UBERON:0001049!1.99e-56!56;UBERON:0005068!1.99e-56!56;UBERON:0006241!1.99e-56!56;UBERON:0007135!1.99e-56!56;UBERON:0003075!1.32e-51!82;UBERON:0007284!1.32e-51!82;UBERON:0000073!1.34e-51!53;UBERON:0002616!1.34e-51!53;UBERON:0002346!1.36e-50!86;UBERON:0002780!3.41e-47!41;UBERON:0001890!3.41e-47!41;UBERON:0003080!3.41e-47!41;UBERON:0006240!3.41e-47!41;UBERON:0003056!1.57e-44!61;UBERON:0001017!4.92e-43!81;UBERON:0003528!1.16e-42!34;UBERON:0002020!1.16e-42!34;UBERON:0001893!3.50e-42!34;UBERON:0001016!6.95e-41!89;UBERON:0000955!1.47e-40!68;UBERON:0006238!1.47e-40!68;UBERON:0001869!2.03e-39!32;UBERON:0002791!2.80e-39!32;UBERON:0010371!3.84e-37!104;UBERON:0007023!4.83e-37!114;UBERON:0001950!7.55e-33!20;UBERON:0002619!1.45e-32!22;UBERON:0010314!1.03e-30!132;UBERON:0000956!5.45e-28!25;UBERON:0000203!5.45e-28!25;UBERON:0011216!5.19e-26!223;UBERON:0004121!2.63e-24!171;UBERON:0000924!2.63e-24!171;UBERON:0006601!2.63e-24!171;UBERON:0000483!1.33e-17!306;UBERON:0000481!1.89e-17!342;UBERON:0000025!2.67e-17!192;UBERON:0000119!3.20e-17!309;UBERON:0000477!1.16e-16!373;UBERON:0000064!1.23e-16!218;UBERON:0000125!1.94e-16!9;UBERON:0002308!1.94e-16!9;UBERON:0009663!4.53e-13!7;UBERON:0002420!9.46e-13!9;UBERON:0007245!9.46e-13!9;UBERON:0010009!9.46e-13!9;UBERON:0010011!9.46e-13!9;UBERON:0000454!9.46e-13!9;UBERON:0000200!1.32e-11!6;UBERON:0002298!1.96e-11!6;UBERON:0004111!2.41e-11!240;UBERON:0003076!1.22e-10!15;UBERON:0003057!1.22e-10!15;UBERON:0001872!3.75e-10!5;UBERON:0002021!4.95e-10!5;UBERON:0001871!7.61e-10!6;UBERON:0000922!4.17e-09!592;UBERON:0000369!6.77e-09!4;UBERON:0002435!6.77e-09!4;UBERON:0000204!6.77e-09!4;UBERON:0010082!6.77e-09!4;UBERON:0000062!8.91e-09!503;UBERON:0000923!1.20e-08!560;UBERON:0010316!1.20e-08!560;UBERON:0005291!1.20e-08!560;UBERON:0006598!1.20e-08!560;UBERON:0010317!1.20e-08!560;UBERON:0002532!1.20e-08!560;UBERON:0002050!2.07e-08!564;UBERON:0005423!2.56e-08!581;UBERON:0000468!3.70e-08!656;UBERON:0004732!4.08e-08!13;UBERON:0000160!7.22e-08!17;UBERON:0001781!1.24e-07!4;UBERON:0000966!2.64e-07!6;UBERON:0005388!2.64e-07!6;UBERON:0001802!2.64e-07!6;UBERON:0005383!2.91e-07!3;UBERON:0005382!2.91e-07!3;UBERON:0000988!7.75e-07!3
|tf_chipseq_enrich=FOXA2#3170;2:16.4203091684435:0.00481068235210548:0.0225818173478154!TRIM28#10155;3:18.5905250452625:0.000155596929725528:0.00196688304812447!USF1#7391;3:6.36149927720796:0.0038840405729056:0.0189846638926236
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}}
}}

Revision as of 15:03, 19 October 2012


Full id: C3393_hereditary_caudate_parietal_breast_locus_putamen_pons



Phase1 CAGE Peaks

Hg19::chr14:100485771..100485833,+p4@EVL
Hg19::chr14:100485908..100485924,+p25@EVL
Hg19::chr14:100485927..100485938,+p29@EVL


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 tube1.99e-5656
neural rod1.99e-5656
future spinal cord1.99e-5656
neural keel1.99e-5656
neural plate1.32e-5182
presumptive neural plate1.32e-5182
regional part of nervous system1.34e-5153
regional part of brain1.34e-5153
neurectoderm1.36e-5086
regional part of forebrain3.41e-4741
forebrain3.41e-4741
anterior neural tube3.41e-4741
future forebrain3.41e-4741
pre-chordal neural plate1.57e-4461
central nervous system4.92e-4381
brain grey matter1.16e-4234
gray matter1.16e-4234
telencephalon3.50e-4234
nervous system6.95e-4189
brain1.47e-4068
future brain1.47e-4068
cerebral hemisphere2.03e-3932
regional part of telencephalon2.80e-3932
ecto-epithelium3.84e-37104
adult organism4.83e-37114
neocortex7.55e-3320
regional part of cerebral cortex1.45e-3222
structure with developmental contribution from neural crest1.03e-30132
cerebral cortex5.45e-2825
pallium5.45e-2825
organ system subdivision5.19e-26223
ectoderm-derived structure2.63e-24171
ectoderm2.63e-24171
presumptive ectoderm2.63e-24171
epithelium1.33e-17306
multi-tissue structure1.89e-17342
tube2.67e-17192
cell layer3.20e-17309
anatomical cluster1.16e-16373
organ part1.23e-16218
neural nucleus1.94e-169
nucleus of brain1.94e-169
telencephalic nucleus4.53e-137
basal ganglion9.46e-139
nuclear complex of neuraxis9.46e-139
aggregate regional part of brain9.46e-139
collection of basal ganglia9.46e-139
cerebral subcortex9.46e-139
gyrus1.32e-116
brainstem1.96e-116
anatomical conduit2.41e-11240
posterior neural tube1.22e-1015
chordal neural plate1.22e-1015
parietal lobe3.75e-105
occipital lobe4.95e-105
temporal lobe7.61e-106
embryo4.17e-09592
corpus striatum6.77e-094
striatum6.77e-094
ventral part of telencephalon6.77e-094
future corpus striatum6.77e-094
organ8.91e-09503
germ layer1.20e-08560
germ layer / neural crest1.20e-08560
embryonic tissue1.20e-08560
presumptive structure1.20e-08560
germ layer / neural crest derived structure1.20e-08560
epiblast (generic)1.20e-08560
embryonic structure2.07e-08564
developing anatomical structure2.56e-08581
multi-cellular organism3.70e-08656
segmental subdivision of nervous system4.08e-0813
intestine7.22e-0817
layer of retina1.24e-074
retina2.64e-076
photoreceptor array2.64e-076
posterior segment of eyeball2.64e-076
caudate-putamen2.91e-073
dorsal striatum2.91e-073
pons7.75e-073


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
FOXA2#3170216.42030916844350.004810682352105480.0225818173478154
TRIM28#10155318.59052504526250.0001555969297255280.00196688304812447
USF1#739136.361499277207960.00388404057290560.0189846638926236



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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