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Coexpression cluster:C3004: Difference between revisions

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|ontology_enrichment_disease=
|ontology_enrichment_disease=
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|ontology_enrichment_uberon=UBERON:0007023!2.55e-51!115;UBERON:0005743!4.74e-41!86;UBERON:0001017!1.57e-40!82;UBERON:0000073!2.74e-39!94;UBERON:0001016!2.74e-39!94;UBERON:0002346!2.18e-36!90;UBERON:0001049!2.28e-36!57;UBERON:0005068!2.28e-36!57;UBERON:0006241!2.28e-36!57;UBERON:0007135!2.28e-36!57;UBERON:0002616!4.21e-36!59;UBERON:0000955!3.58e-35!69;UBERON:0006238!3.58e-35!69;UBERON:0003075!1.08e-34!86;UBERON:0007284!1.08e-34!86;UBERON:0000924!1.91e-32!173;UBERON:0006601!1.91e-32!173;UBERON:0000153!2.15e-31!129;UBERON:0007811!2.15e-31!129;UBERON:0000033!2.76e-31!123;UBERON:0004121!8.42e-31!169;UBERON:0003080!5.42e-29!42;UBERON:0002780!1.50e-28!41;UBERON:0001890!1.50e-28!41;UBERON:0006240!1.50e-28!41;UBERON:0003056!8.03e-27!61;UBERON:0002020!2.38e-24!34;UBERON:0003528!2.38e-24!34;UBERON:0001893!2.38e-24!34;UBERON:0001869!9.90e-24!32;UBERON:0002791!1.23e-23!33;UBERON:0000956!2.07e-18!25;UBERON:0000203!2.07e-18!25;UBERON:0002619!5.77e-17!22;UBERON:0001950!2.43e-15!20;UBERON:0000475!1.12e-14!365;UBERON:0000468!1.65e-14!659;UBERON:0000481!2.68e-14!347;UBERON:0000062!1.38e-12!511;UBERON:0000922!1.64e-12!612;UBERON:0002050!1.66e-10!605;UBERON:0005423!1.66e-10!605;UBERON:0000923!3.92e-10!604;UBERON:0005291!3.92e-10!604;UBERON:0006598!3.92e-10!604;UBERON:0002532!3.92e-10!604;UBERON:0000064!7.17e-10!219;UBERON:0000467!1.24e-08!625;UBERON:0003076!1.60e-08!15;UBERON:0003057!1.60e-08!15;UBERON:0000480!1.65e-08!626;UBERON:0000477!3.51e-08!286;UBERON:0000483!4.86e-08!309;UBERON:0002420!1.15e-07!9;UBERON:0007245!1.15e-07!9;UBERON:0010009!1.15e-07!9;UBERON:0010011!1.15e-07!9;UBERON:0000454!1.15e-07!9;UBERON:0000119!1.24e-07!312;UBERON:0002308!2.25e-07!9;UBERON:0000125!2.25e-07!9;UBERON:0004733!3.35e-07!12;UBERON:0002028!3.35e-07!12;UBERON:0007277!3.35e-07!12;UBERON:0000059!3.56e-07!11;UBERON:0001871!4.79e-07!7
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}}
}}

Revision as of 11:31, 5 September 2012


Full id: C3004_smooth_putamen_bladder_vagina_neuroectodermal_caudate_salivary



Phase1 CAGE Peaks

Hg19::chr10:18429301..18429338,+p1@CACNB2
Hg19::chr10:18429342..18429359,+p3@CACNB2
Hg19::chr10:18429658..18429670,+p14@CACNB2


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 organism2.55e-51115
central nervous system1.57e-4082
regional part of nervous system2.74e-3994
nervous system2.74e-3994
neurectoderm2.18e-3690
neural tube2.28e-3657
neural rod2.28e-3657
future spinal cord2.28e-3657
neural keel2.28e-3657
regional part of brain4.21e-3659
brain3.58e-3569
future brain3.58e-3569
neural plate1.08e-3486
presumptive neural plate1.08e-3486
ectoderm1.91e-32173
presumptive ectoderm1.91e-32173
anterior region of body2.15e-31129
craniocervical region2.15e-31129
head2.76e-31123
ectoderm-derived structure8.42e-31169
anterior neural tube5.42e-2942
regional part of forebrain1.50e-2841
forebrain1.50e-2841
future forebrain1.50e-2841
pre-chordal neural plate8.03e-2761
gray matter2.38e-2434
brain grey matter2.38e-2434
telencephalon2.38e-2434
cerebral hemisphere9.90e-2432
regional part of telencephalon1.23e-2333
cerebral cortex2.07e-1825
pallium2.07e-1825
regional part of cerebral cortex5.77e-1722
neocortex2.43e-1520
organism subdivision1.12e-14365
multi-cellular organism1.65e-14659
multi-tissue structure2.68e-14347
organ1.38e-12511
embryo1.64e-12612
embryonic structure1.66e-10605
developing anatomical structure1.66e-10605
germ layer3.92e-10604
embryonic tissue3.92e-10604
presumptive structure3.92e-10604
epiblast (generic)3.92e-10604
organ part7.17e-10219
anatomical system1.24e-08625
posterior neural tube1.60e-0815
chordal neural plate1.60e-0815
anatomical group1.65e-08626
anatomical cluster3.51e-08286
epithelium4.86e-08309
basal ganglion1.15e-079
nuclear complex of neuraxis1.15e-079
aggregate regional part of brain1.15e-079
collection of basal ganglia1.15e-079
cerebral subcortex1.15e-079
cell layer1.24e-07312
nucleus of brain2.25e-079
neural nucleus2.25e-079
segmental subdivision of hindbrain3.35e-0712
hindbrain3.35e-0712
presumptive hindbrain3.35e-0712
large intestine3.56e-0711
temporal lobe4.79e-077


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#1066435.360256373075030.0064925092527670.0278160222279088



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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