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Coexpression cluster:C1873: Difference between revisions

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|id=C1873
|id=C1873
|ontology_enrichment_celltype=
|ontology_enrichment_celltype=
|ontology_enrichment_disease=DOID:0050687!3.29e-15!143;DOID:305!5.17e-12!106;DOID:162!1.42e-08!235;DOID:14566!6.28e-08!239
|ontology_enrichment_disease=DOID:0050687!2.74e-14!143;DOID:305!5.80e-11!106;DOID:162!5.77e-07!235
|ontology_enrichment_uberon=UBERON:0005743!5.47e-26!86;UBERON:0000073!8.38e-25!94;UBERON:0001016!8.38e-25!94;UBERON:0001049!1.13e-24!57;UBERON:0005068!1.13e-24!57;UBERON:0006241!1.13e-24!57;UBERON:0007135!1.13e-24!57;UBERON:0001017!1.25e-24!82;UBERON:0002346!1.11e-22!90;UBERON:0007023!3.15e-22!115;UBERON:0003075!6.80e-22!86;UBERON:0007284!6.80e-22!86;UBERON:0002780!1.15e-20!41;UBERON:0001890!1.15e-20!41;UBERON:0006240!1.15e-20!41;UBERON:0000955!1.72e-20!69;UBERON:0006238!1.72e-20!69;UBERON:0003080!1.76e-19!42;UBERON:0002616!1.47e-18!59;UBERON:0002020!9.66e-18!34;UBERON:0003528!9.66e-18!34;UBERON:0001893!1.45e-17!34;UBERON:0001869!3.91e-17!32;UBERON:0002791!5.33e-17!33;UBERON:0000025!1.36e-16!194;UBERON:0003056!4.41e-15!61;UBERON:0004111!7.30e-15!241;UBERON:0000924!5.78e-14!173;UBERON:0006601!5.78e-14!173;UBERON:0002619!7.50e-14!22;UBERON:0000956!8.29e-14!25;UBERON:0000203!8.29e-14!25;UBERON:0004121!3.04e-13!169;UBERON:0001950!5.79e-13!20;UBERON:0000483!9.43e-12!309;UBERON:0000119!2.22e-11!312;UBERON:0000033!6.66e-11!123;UBERON:0000477!8.76e-11!286;UBERON:0000153!9.73e-11!129;UBERON:0007811!9.73e-11!129;UBERON:0000481!2.15e-09!347;UBERON:0000064!6.03e-09!219;UBERON:0000475!1.08e-08!365;UBERON:0000468!2.89e-08!659;UBERON:0000922!4.77e-08!612;UBERON:0000062!1.21e-07!511;UBERON:0000467!1.29e-07!625;UBERON:0000480!2.03e-07!626
|ontology_enrichment_uberon=UBERON:0001017!4.76e-32!81;UBERON:0001049!4.18e-31!56;UBERON:0005068!4.18e-31!56;UBERON:0006241!4.18e-31!56;UBERON:0007135!4.18e-31!56;UBERON:0001016!2.41e-30!89;UBERON:0000073!3.35e-30!53;UBERON:0002616!3.35e-30!53;UBERON:0002780!4.49e-29!41;UBERON:0001890!4.49e-29!41;UBERON:0003080!4.49e-29!41;UBERON:0006240!4.49e-29!41;UBERON:0000955!6.20e-29!68;UBERON:0006238!6.20e-29!68;UBERON:0003528!4.24e-24!34;UBERON:0002020!4.24e-24!34;UBERON:0002346!5.01e-24!86;UBERON:0001893!8.54e-24!34;UBERON:0007023!1.55e-23!114;UBERON:0001869!6.46e-23!32;UBERON:0003075!1.18e-22!82;UBERON:0007284!1.18e-22!82;UBERON:0002791!1.97e-22!32;UBERON:0003056!1.69e-18!61;UBERON:0010371!2.13e-18!104;UBERON:0011216!2.78e-18!223;UBERON:0001950!1.00e-17!20;UBERON:0002619!2.40e-17!22;UBERON:0000956!3.60e-17!25;UBERON:0000203!3.60e-17!25;UBERON:0004121!4.58e-17!171;UBERON:0000924!4.58e-17!171;UBERON:0006601!4.58e-17!171;UBERON:0010314!1.70e-15!132;UBERON:0000477!1.56e-08!373;UBERON:0002420!1.68e-08!9;UBERON:0007245!1.68e-08!9;UBERON:0010009!1.68e-08!9;UBERON:0010011!1.68e-08!9;UBERON:0000454!1.68e-08!9;UBERON:0000125!1.96e-08!9;UBERON:0002308!1.96e-08!9;UBERON:0000025!1.97e-08!192;UBERON:0000200!1.31e-07!6;UBERON:0000064!3.00e-07!218;UBERON:0000481!8.52e-07!342;UBERON:0009663!8.62e-07!7
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}}
}}

Revision as of 11:47, 19 October 2012


Full id: C1873_skeletal_MCF7_serous_left_brain_heart_tongue



Phase1 CAGE Peaks

Hg19::chr20:62127314..62127345,-p6@EEF1A2
Hg19::chr20:62128967..62129009,+p@chr20:62128967..62129009
+
Hg19::chr20:62129099..62129111,-p10@EEF1A2
Hg19::chr20:62129135..62129160,-p7@EEF1A2
Hg19::chr20:62130428..62130472,-p1@EEF1A2


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>disease_data<br>

Uber Anatomy
Ontology termp-valuen
central nervous system4.76e-3281
neural tube4.18e-3156
neural rod4.18e-3156
future spinal cord4.18e-3156
neural keel4.18e-3156
nervous system2.41e-3089
regional part of nervous system3.35e-3053
regional part of brain3.35e-3053
regional part of forebrain4.49e-2941
forebrain4.49e-2941
anterior neural tube4.49e-2941
future forebrain4.49e-2941
brain6.20e-2968
future brain6.20e-2968
brain grey matter4.24e-2434
gray matter4.24e-2434
neurectoderm5.01e-2486
telencephalon8.54e-2434
adult organism1.55e-23114
cerebral hemisphere6.46e-2332
neural plate1.18e-2282
presumptive neural plate1.18e-2282
regional part of telencephalon1.97e-2232
pre-chordal neural plate1.69e-1861
ecto-epithelium2.13e-18104
organ system subdivision2.78e-18223
neocortex1.00e-1720
regional part of cerebral cortex2.40e-1722
cerebral cortex3.60e-1725
pallium3.60e-1725
ectoderm-derived structure4.58e-17171
ectoderm4.58e-17171
presumptive ectoderm4.58e-17171
structure with developmental contribution from neural crest1.70e-15132
anatomical cluster1.56e-08373
basal ganglion1.68e-089
nuclear complex of neuraxis1.68e-089
aggregate regional part of brain1.68e-089
collection of basal ganglia1.68e-089
cerebral subcortex1.68e-089
neural nucleus1.96e-089
nucleus of brain1.96e-089
tube1.97e-08192
gyrus1.31e-076
organ part3.00e-07218
multi-tissue structure8.52e-07342
telencephalic nucleus8.62e-077
Disease
Ontology termp-valuen
cell type cancer2.74e-14143
carcinoma5.80e-11106
cancer5.77e-07235


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

No analysis results for this cluster

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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