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Coexpression cluster:C3619: Difference between revisions

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|ontology_enrichment_disease=
|ontology_enrichment_disease=
|ontology_enrichment_uberon=UBERON:0001049!1.78e-27!57;UBERON:0005068!1.78e-27!57;UBERON:0006241!1.78e-27!57;UBERON:0007135!1.78e-27!57;UBERON:0002616!2.28e-22!59;UBERON:0001017!2.55e-22!82;UBERON:0000073!3.68e-22!94;UBERON:0001016!3.68e-22!94;UBERON:0005743!4.16e-21!86;UBERON:0000955!5.55e-21!69;UBERON:0006238!5.55e-21!69;UBERON:0002780!8.84e-21!41;UBERON:0001890!8.84e-21!41;UBERON:0006240!8.84e-21!41;UBERON:0003080!1.16e-19!42;UBERON:0002346!3.45e-19!90;UBERON:0003075!2.12e-18!86;UBERON:0007284!2.12e-18!86;UBERON:0007023!1.45e-17!115;UBERON:0002020!7.68e-17!34;UBERON:0003528!7.68e-17!34;UBERON:0001893!9.29e-17!34;UBERON:0001869!2.37e-16!32;UBERON:0002791!3.94e-16!33;UBERON:0000924!6.92e-16!173;UBERON:0006601!6.92e-16!173;UBERON:0000025!2.75e-15!194;UBERON:0004121!3.98e-15!169;UBERON:0002619!1.06e-14!22;UBERON:0000033!2.59e-14!123;UBERON:0000153!3.57e-14!129;UBERON:0007811!3.57e-14!129;UBERON:0001950!2.03e-13!20;UBERON:0000475!1.26e-12!365;UBERON:0004111!3.61e-12!241;UBERON:0000477!3.98e-12!286;UBERON:0000956!7.30e-12!25;UBERON:0000203!7.30e-12!25;UBERON:0003056!7.33e-12!61;UBERON:0000481!1.33e-11!347;UBERON:0000483!2.34e-11!309;UBERON:0000119!5.08e-11!312;UBERON:0003076!5.53e-09!15;UBERON:0003057!5.53e-09!15;UBERON:0000064!7.76e-09!219;UBERON:0004732!1.58e-07!13;UBERON:0004733!2.64e-07!12;UBERON:0002028!2.64e-07!12;UBERON:0007277!2.64e-07!12
|ontology_enrichment_uberon=UBERON:0001049!1.78e-27!57;UBERON:0005068!1.78e-27!57;UBERON:0006241!1.78e-27!57;UBERON:0007135!1.78e-27!57;UBERON:0002616!2.28e-22!59;UBERON:0001017!2.55e-22!82;UBERON:0000073!3.68e-22!94;UBERON:0001016!3.68e-22!94;UBERON:0005743!4.16e-21!86;UBERON:0000955!5.55e-21!69;UBERON:0006238!5.55e-21!69;UBERON:0002780!8.84e-21!41;UBERON:0001890!8.84e-21!41;UBERON:0006240!8.84e-21!41;UBERON:0003080!1.16e-19!42;UBERON:0002346!3.45e-19!90;UBERON:0003075!2.12e-18!86;UBERON:0007284!2.12e-18!86;UBERON:0007023!1.45e-17!115;UBERON:0002020!7.68e-17!34;UBERON:0003528!7.68e-17!34;UBERON:0001893!9.29e-17!34;UBERON:0001869!2.37e-16!32;UBERON:0002791!3.94e-16!33;UBERON:0000924!6.92e-16!173;UBERON:0006601!6.92e-16!173;UBERON:0000025!2.75e-15!194;UBERON:0004121!3.98e-15!169;UBERON:0002619!1.06e-14!22;UBERON:0000033!2.59e-14!123;UBERON:0000153!3.57e-14!129;UBERON:0007811!3.57e-14!129;UBERON:0001950!2.03e-13!20;UBERON:0000475!1.26e-12!365;UBERON:0004111!3.61e-12!241;UBERON:0000477!3.98e-12!286;UBERON:0000956!7.30e-12!25;UBERON:0000203!7.30e-12!25;UBERON:0003056!7.33e-12!61;UBERON:0000481!1.33e-11!347;UBERON:0000483!2.34e-11!309;UBERON:0000119!5.08e-11!312;UBERON:0003076!5.53e-09!15;UBERON:0003057!5.53e-09!15;UBERON:0000064!7.76e-09!219;UBERON:0004732!1.58e-07!13;UBERON:0004733!2.64e-07!12;UBERON:0002028!2.64e-07!12;UBERON:0007277!2.64e-07!12
|tf_chipseq_enrich=TRIM28#10155;2:12.3936833635083:0.00836834412943847:0.0329009747227234
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}}
}}

Revision as of 12:38, 5 September 2012


Full id: C3619_cerebellum_occipital_caudate_putamen_Fibroblast_medial_amygdala



Phase1 CAGE Peaks

Hg19::chr17:26698422..26698461,+p6@SARM1
Hg19::chr3:141105795..141105814,+p@chr3:141105795..141105814
+
Hg19::chr3:141105820..141105861,+p@chr3:141105820..141105861
+


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 tube1.78e-2757
neural rod1.78e-2757
future spinal cord1.78e-2757
neural keel1.78e-2757
regional part of brain2.28e-2259
central nervous system2.55e-2282
regional part of nervous system3.68e-2294
nervous system3.68e-2294
brain5.55e-2169
future brain5.55e-2169
regional part of forebrain8.84e-2141
forebrain8.84e-2141
future forebrain8.84e-2141
anterior neural tube1.16e-1942
neurectoderm3.45e-1990
neural plate2.12e-1886
presumptive neural plate2.12e-1886
adult organism1.45e-17115
gray matter7.68e-1734
brain grey matter7.68e-1734
telencephalon9.29e-1734
cerebral hemisphere2.37e-1632
regional part of telencephalon3.94e-1633
ectoderm6.92e-16173
presumptive ectoderm6.92e-16173
tube2.75e-15194
ectoderm-derived structure3.98e-15169
regional part of cerebral cortex1.06e-1422
head2.59e-14123
anterior region of body3.57e-14129
craniocervical region3.57e-14129
neocortex2.03e-1320
organism subdivision1.26e-12365
anatomical conduit3.61e-12241
anatomical cluster3.98e-12286
cerebral cortex7.30e-1225
pallium7.30e-1225
pre-chordal neural plate7.33e-1261
multi-tissue structure1.33e-11347
epithelium2.34e-11309
cell layer5.08e-11312
posterior neural tube5.53e-0915
chordal neural plate5.53e-0915
organ part7.76e-09219
segmental subdivision of nervous system1.58e-0713
segmental subdivision of hindbrain2.64e-0712
hindbrain2.64e-0712
presumptive hindbrain2.64e-0712


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)

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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
TRIM28#10155212.39368336350830.008368344129438470.0329009747227234



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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