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Coexpression cluster:C2111: Difference between revisions

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|full_id=C2111_retinoblastoma_insula_medial_occipital_parietal_brain_temporal
|full_id=C2111_retinoblastoma_insula_medial_occipital_parietal_brain_temporal
|id=C2111
|id=C2111
|ontology_enrichment_celltype=CL:0002076!1.02e-11!43;CL:0000223!8.23e-08!59;CL:0002251!1.52e-07!21
|ontology_enrichment_celltype=
|ontology_enrichment_disease=DOID:1749!4.14e-10!14
|ontology_enrichment_disease=DOID:1749!2.81e-08!14
|ontology_enrichment_uberon=UBERON:0007023!1.76e-27!115;UBERON:0001869!1.92e-22!32;UBERON:0003080!6.89e-22!42;UBERON:0001893!9.77e-22!34;UBERON:0002780!1.92e-21!41;UBERON:0001890!1.92e-21!41;UBERON:0006240!1.92e-21!41;UBERON:0002791!9.51e-21!33;UBERON:0002619!2.37e-20!22;UBERON:0001950!5.65e-19!20;UBERON:0002020!1.42e-18!34;UBERON:0003528!1.42e-18!34;UBERON:0000153!1.38e-17!129;UBERON:0007811!1.38e-17!129;UBERON:0000956!6.71e-17!25;UBERON:0000203!6.71e-17!25;UBERON:0000033!1.29e-16!123;UBERON:0003056!1.20e-15!61;UBERON:0004121!3.34e-15!169;UBERON:0001049!3.73e-15!57;UBERON:0005068!3.73e-15!57;UBERON:0006241!3.73e-15!57;UBERON:0007135!3.73e-15!57;UBERON:0001017!1.44e-14!82;UBERON:0000955!2.49e-14!69;UBERON:0006238!2.49e-14!69;UBERON:0000924!2.85e-14!173;UBERON:0006601!2.85e-14!173;UBERON:0005743!4.67e-14!86;UBERON:0002616!1.84e-13!59;UBERON:0000073!6.63e-12!94;UBERON:0001016!6.63e-12!94;UBERON:0003075!2.64e-10!86;UBERON:0007284!2.64e-10!86;UBERON:0004119!3.55e-10!169;UBERON:0000925!3.55e-10!169;UBERON:0006595!3.55e-10!169;UBERON:0000064!2.88e-09!219;UBERON:0002346!3.06e-09!90;UBERON:0000161!9.09e-09!35;UBERON:0001871!9.59e-09!7;UBERON:0001004!2.00e-08!72;UBERON:0000166!2.27e-08!21;UBERON:0001007!2.40e-08!155;UBERON:0001555!2.40e-08!155;UBERON:0007026!2.40e-08!155;UBERON:0000200!1.02e-07!6;UBERON:0004921!2.09e-07!129;UBERON:0004185!2.09e-07!129;UBERON:0002420!7.24e-07!9;UBERON:0007245!7.24e-07!9;UBERON:0010009!7.24e-07!9;UBERON:0010011!7.24e-07!9;UBERON:0000454!7.24e-07!9;UBERON:0000062!7.65e-07!511
|ontology_enrichment_uberon=UBERON:0001869!9.43e-40!32;UBERON:0001893!5.11e-37!34;UBERON:0002791!2.88e-36!32;UBERON:0002619!9.31e-35!22;UBERON:0001950!1.22e-34!20;UBERON:0002780!1.75e-34!41;UBERON:0001890!1.75e-34!41;UBERON:0003080!1.75e-34!41;UBERON:0006240!1.75e-34!41;UBERON:0003528!9.37e-34!34;UBERON:0002020!9.37e-34!34;UBERON:0007023!4.18e-33!114;UBERON:0000956!4.78e-30!25;UBERON:0000203!4.78e-30!25;UBERON:0003056!3.13e-28!61;UBERON:0000955!5.68e-28!68;UBERON:0006238!5.68e-28!68;UBERON:0000073!7.73e-27!53;UBERON:0002616!7.73e-27!53;UBERON:0001017!3.21e-25!81;UBERON:0001049!5.69e-25!56;UBERON:0005068!5.69e-25!56;UBERON:0006241!5.69e-25!56;UBERON:0007135!5.69e-25!56;UBERON:0001016!1.00e-21!89;UBERON:0003075!4.67e-20!82;UBERON:0007284!4.67e-20!82;UBERON:0002346!1.06e-18!86;UBERON:0011216!1.97e-18!223;UBERON:0010371!2.33e-18!104;UBERON:0004121!2.61e-18!171;UBERON:0000924!2.61e-18!171;UBERON:0006601!2.61e-18!171;UBERON:0000200!6.31e-15!6;UBERON:0010314!1.04e-12!132;UBERON:0001871!2.30e-12!6;UBERON:0002420!1.48e-11!9;UBERON:0007245!1.48e-11!9;UBERON:0010009!1.48e-11!9;UBERON:0010011!1.48e-11!9;UBERON:0000454!1.48e-11!9;UBERON:0000064!4.50e-11!218;UBERON:0000477!2.34e-09!373;UBERON:0000481!1.26e-08!342;UBERON:0001872!2.07e-08!5;UBERON:0002021!2.07e-08!5;UBERON:0001870!2.46e-08!3;UBERON:0000349!4.44e-08!5;UBERON:0000062!6.35e-08!503;UBERON:0009663!1.08e-07!7;UBERON:0004111!1.15e-07!240
|tf_chipseq_enrich=GATA3#2625;2:13.618258178603:0.0076966520809334:0.0316855471906896
|tf_chipseq_enrich=GATA3#2625;2:13.618258178603:0.0076966520809334:0.0316855471906896
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}}
}}

Revision as of 12:04, 19 October 2012


Full id: C2111_retinoblastoma_insula_medial_occipital_parietal_brain_temporal



Phase1 CAGE Peaks

Hg19::chr11:128894012..128894023,-p11@ARHGAP32
Hg19::chr11:128894024..128894050,-p3@ARHGAP32
Hg19::chr19:35633194..35633212,+p@chr19:35633194..35633212
+
Hg19::chr22:43820905..43820917,+p10@MPPED1


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
cerebral hemisphere9.43e-4032
telencephalon5.11e-3734
regional part of telencephalon2.88e-3632
regional part of cerebral cortex9.31e-3522
neocortex1.22e-3420
regional part of forebrain1.75e-3441
forebrain1.75e-3441
anterior neural tube1.75e-3441
future forebrain1.75e-3441
brain grey matter9.37e-3434
gray matter9.37e-3434
adult organism4.18e-33114
cerebral cortex4.78e-3025
pallium4.78e-3025
pre-chordal neural plate3.13e-2861
brain5.68e-2868
future brain5.68e-2868
regional part of nervous system7.73e-2753
regional part of brain7.73e-2753
central nervous system3.21e-2581
neural tube5.69e-2556
neural rod5.69e-2556
future spinal cord5.69e-2556
neural keel5.69e-2556
nervous system1.00e-2189
neural plate4.67e-2082
presumptive neural plate4.67e-2082
neurectoderm1.06e-1886
organ system subdivision1.97e-18223
ecto-epithelium2.33e-18104
ectoderm-derived structure2.61e-18171
ectoderm2.61e-18171
presumptive ectoderm2.61e-18171
gyrus6.31e-156
structure with developmental contribution from neural crest1.04e-12132
temporal lobe2.30e-126
basal ganglion1.48e-119
nuclear complex of neuraxis1.48e-119
aggregate regional part of brain1.48e-119
collection of basal ganglia1.48e-119
cerebral subcortex1.48e-119
organ part4.50e-11218
anatomical cluster2.34e-09373
multi-tissue structure1.26e-08342
parietal lobe2.07e-085
occipital lobe2.07e-085
frontal cortex2.46e-083
limbic system4.44e-085
organ6.35e-08503
telencephalic nucleus1.08e-077
anatomical conduit1.15e-07240
Disease
Ontology termp-valuen
squamous cell carcinoma2.81e-0814


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
GATA3#2625213.6182581786030.00769665208093340.0316855471906896



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.

Retrieved from "http://f5-webapp4.gsc.riken.jp/resource_browser/index.php?title=Coexpression_cluster:C2111&oldid=2248183"