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Coexpression cluster:C4417: Difference between revisions

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|ontology_enrichment_disease=
|ontology_enrichment_disease=
|ontology_enrichment_uberon=UBERON:0007023!5.19e-26!115;UBERON:0000073!1.60e-25!94;UBERON:0001016!1.60e-25!94;UBERON:0001017!2.06e-25!82;UBERON:0004121!4.35e-25!169;UBERON:0005743!6.79e-25!86;UBERON:0000924!8.36e-25!173;UBERON:0006601!8.36e-25!173;UBERON:0001049!1.32e-23!57;UBERON:0005068!1.32e-23!57;UBERON:0006241!1.32e-23!57;UBERON:0007135!1.32e-23!57;UBERON:0002616!7.42e-22!59;UBERON:0000955!1.30e-21!69;UBERON:0006238!1.30e-21!69;UBERON:0003080!2.32e-17!42;UBERON:0002780!2.85e-17!41;UBERON:0001890!2.85e-17!41;UBERON:0006240!2.85e-17!41;UBERON:0000153!9.78e-17!129;UBERON:0007811!9.78e-17!129;UBERON:0000033!1.35e-16!123;UBERON:0003075!3.12e-16!86;UBERON:0007284!3.12e-16!86;UBERON:0002346!8.70e-16!90;UBERON:0002020!1.25e-15!34;UBERON:0003528!1.25e-15!34;UBERON:0001893!2.80e-15!34;UBERON:0001869!5.97e-15!32;UBERON:0002791!9.86e-15!33;UBERON:0002619!2.03e-12!22;UBERON:0001950!8.97e-12!20;UBERON:0004111!1.10e-11!241;UBERON:0000956!2.39e-11!25;UBERON:0000203!2.39e-11!25;UBERON:0003056!9.10e-11!61;UBERON:0000119!4.27e-10!312;UBERON:0000483!5.80e-10!309;UBERON:0000025!8.76e-10!194;UBERON:0000064!1.35e-09!219;UBERON:0000475!4.78e-09!365;UBERON:0000477!7.40e-08!286;UBERON:0000467!1.83e-07!625;UBERON:0003076!1.85e-07!15;UBERON:0003057!1.85e-07!15;UBERON:0000480!2.86e-07!626
|ontology_enrichment_uberon=UBERON:0007023!5.19e-26!115;UBERON:0000073!1.60e-25!94;UBERON:0001016!1.60e-25!94;UBERON:0001017!2.06e-25!82;UBERON:0004121!4.35e-25!169;UBERON:0005743!6.79e-25!86;UBERON:0000924!8.36e-25!173;UBERON:0006601!8.36e-25!173;UBERON:0001049!1.32e-23!57;UBERON:0005068!1.32e-23!57;UBERON:0006241!1.32e-23!57;UBERON:0007135!1.32e-23!57;UBERON:0002616!7.42e-22!59;UBERON:0000955!1.30e-21!69;UBERON:0006238!1.30e-21!69;UBERON:0003080!2.32e-17!42;UBERON:0002780!2.85e-17!41;UBERON:0001890!2.85e-17!41;UBERON:0006240!2.85e-17!41;UBERON:0000153!9.78e-17!129;UBERON:0007811!9.78e-17!129;UBERON:0000033!1.35e-16!123;UBERON:0003075!3.12e-16!86;UBERON:0007284!3.12e-16!86;UBERON:0002346!8.70e-16!90;UBERON:0002020!1.25e-15!34;UBERON:0003528!1.25e-15!34;UBERON:0001893!2.80e-15!34;UBERON:0001869!5.97e-15!32;UBERON:0002791!9.86e-15!33;UBERON:0002619!2.03e-12!22;UBERON:0001950!8.97e-12!20;UBERON:0004111!1.10e-11!241;UBERON:0000956!2.39e-11!25;UBERON:0000203!2.39e-11!25;UBERON:0003056!9.10e-11!61;UBERON:0000119!4.27e-10!312;UBERON:0000483!5.80e-10!309;UBERON:0000025!8.76e-10!194;UBERON:0000064!1.35e-09!219;UBERON:0000475!4.78e-09!365;UBERON:0000477!7.40e-08!286;UBERON:0000467!1.83e-07!625;UBERON:0003076!1.85e-07!15;UBERON:0003057!1.85e-07!15;UBERON:0000480!2.86e-07!626
|tf_chipseq_enrich=YY1#7528;3:4.91117074985386:0.00844145534180826:0.0330664299168522
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}}
}}

Revision as of 13:32, 5 September 2012


Full id: C4417_normal_duodenum_brain_temporal_pituitary_putamen_Placental



Phase1 CAGE Peaks

Hg19::chr4:4388727..4388736,+p5@D4S234E
Hg19::chr4:4388780..4388789,+p7@D4S234E
Hg19::chr4:4388805..4388855,+p1@D4S234E


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 organism5.19e-26115
regional part of nervous system1.60e-2594
nervous system1.60e-2594
central nervous system2.06e-2582
ectoderm-derived structure4.35e-25169
ectoderm8.36e-25173
presumptive ectoderm8.36e-25173
neural tube1.32e-2357
neural rod1.32e-2357
future spinal cord1.32e-2357
neural keel1.32e-2357
regional part of brain7.42e-2259
brain1.30e-2169
future brain1.30e-2169
anterior neural tube2.32e-1742
regional part of forebrain2.85e-1741
forebrain2.85e-1741
future forebrain2.85e-1741
anterior region of body9.78e-17129
craniocervical region9.78e-17129
head1.35e-16123
neural plate3.12e-1686
presumptive neural plate3.12e-1686
neurectoderm8.70e-1690
gray matter1.25e-1534
brain grey matter1.25e-1534
telencephalon2.80e-1534
cerebral hemisphere5.97e-1532
regional part of telencephalon9.86e-1533
regional part of cerebral cortex2.03e-1222
neocortex8.97e-1220
anatomical conduit1.10e-11241
cerebral cortex2.39e-1125
pallium2.39e-1125
pre-chordal neural plate9.10e-1161
cell layer4.27e-10312
epithelium5.80e-10309
tube8.76e-10194
organ part1.35e-09219
organism subdivision4.78e-09365
anatomical cluster7.40e-08286
anatomical system1.83e-07625
posterior neural tube1.85e-0715
chordal neural plate1.85e-0715
anatomical group2.86e-07626


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
YY1#752834.911170749853860.008441455341808260.0330664299168522



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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