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Coexpression cluster:C4611: Difference between revisions

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|ontology_enrichment_disease=
|ontology_enrichment_disease=
|ontology_enrichment_uberon=UBERON:0001049!8.09e-42!57;UBERON:0005068!8.09e-42!57;UBERON:0006241!8.09e-42!57;UBERON:0007135!8.09e-42!57;UBERON:0000073!9.67e-39!94;UBERON:0001016!9.67e-39!94;UBERON:0001017!2.83e-36!82;UBERON:0003075!8.44e-36!86;UBERON:0007284!8.44e-36!86;UBERON:0005743!2.84e-35!86;UBERON:0000955!2.14e-34!69;UBERON:0006238!2.14e-34!69;UBERON:0002616!2.99e-34!59;UBERON:0002346!2.61e-33!90;UBERON:0001869!1.42e-32!32;UBERON:0002780!3.71e-32!41;UBERON:0001890!3.71e-32!41;UBERON:0006240!3.71e-32!41;UBERON:0002020!3.82e-32!34;UBERON:0003528!3.82e-32!34;UBERON:0001893!5.54e-32!34;UBERON:0003080!4.28e-31!42;UBERON:0002791!9.84e-31!33;UBERON:0001950!1.30e-27!20;UBERON:0003056!2.61e-27!61;UBERON:0002619!5.45e-27!22;UBERON:0000956!1.02e-24!25;UBERON:0000203!1.02e-24!25;UBERON:0004121!6.26e-24!169;UBERON:0000924!7.99e-23!173;UBERON:0006601!7.99e-23!173;UBERON:0000033!5.61e-21!123;UBERON:0000153!3.99e-19!129;UBERON:0007811!3.99e-19!129;UBERON:0007023!3.28e-17!115;UBERON:0000064!1.50e-12!219;UBERON:0003076!1.36e-11!15;UBERON:0003057!1.36e-11!15;UBERON:0001871!3.49e-11!7;UBERON:0002420!3.86e-09!9;UBERON:0007245!3.86e-09!9;UBERON:0010009!3.86e-09!9;UBERON:0010011!3.86e-09!9;UBERON:0000454!3.86e-09!9;UBERON:0000200!4.56e-09!6;UBERON:0004733!6.67e-09!12;UBERON:0002028!6.67e-09!12;UBERON:0007277!6.67e-09!12;UBERON:0002308!8.04e-09!9;UBERON:0000125!8.04e-09!9;UBERON:0004732!5.12e-08!13;UBERON:0002021!6.08e-08!5;UBERON:0001872!7.97e-08!5;UBERON:0000483!2.54e-07!309;UBERON:0000025!2.78e-07!194;UBERON:0000119!4.63e-07!312;UBERON:0009663!8.86e-07!7
|ontology_enrichment_uberon=UBERON:0001049!8.09e-42!57;UBERON:0005068!8.09e-42!57;UBERON:0006241!8.09e-42!57;UBERON:0007135!8.09e-42!57;UBERON:0000073!9.67e-39!94;UBERON:0001016!9.67e-39!94;UBERON:0001017!2.83e-36!82;UBERON:0003075!8.44e-36!86;UBERON:0007284!8.44e-36!86;UBERON:0005743!2.84e-35!86;UBERON:0000955!2.14e-34!69;UBERON:0006238!2.14e-34!69;UBERON:0002616!2.99e-34!59;UBERON:0002346!2.61e-33!90;UBERON:0001869!1.42e-32!32;UBERON:0002780!3.71e-32!41;UBERON:0001890!3.71e-32!41;UBERON:0006240!3.71e-32!41;UBERON:0002020!3.82e-32!34;UBERON:0003528!3.82e-32!34;UBERON:0001893!5.54e-32!34;UBERON:0003080!4.28e-31!42;UBERON:0002791!9.84e-31!33;UBERON:0001950!1.30e-27!20;UBERON:0003056!2.61e-27!61;UBERON:0002619!5.45e-27!22;UBERON:0000956!1.02e-24!25;UBERON:0000203!1.02e-24!25;UBERON:0004121!6.26e-24!169;UBERON:0000924!7.99e-23!173;UBERON:0006601!7.99e-23!173;UBERON:0000033!5.61e-21!123;UBERON:0000153!3.99e-19!129;UBERON:0007811!3.99e-19!129;UBERON:0007023!3.28e-17!115;UBERON:0000064!1.50e-12!219;UBERON:0003076!1.36e-11!15;UBERON:0003057!1.36e-11!15;UBERON:0001871!3.49e-11!7;UBERON:0002420!3.86e-09!9;UBERON:0007245!3.86e-09!9;UBERON:0010009!3.86e-09!9;UBERON:0010011!3.86e-09!9;UBERON:0000454!3.86e-09!9;UBERON:0000200!4.56e-09!6;UBERON:0004733!6.67e-09!12;UBERON:0002028!6.67e-09!12;UBERON:0007277!6.67e-09!12;UBERON:0002308!8.04e-09!9;UBERON:0000125!8.04e-09!9;UBERON:0004732!5.12e-08!13;UBERON:0002021!6.08e-08!5;UBERON:0001872!7.97e-08!5;UBERON:0000483!2.54e-07!309;UBERON:0000025!2.78e-07!194;UBERON:0000119!4.63e-07!312;UBERON:0009663!8.86e-07!7
|tf_chipseq_enrich=SUZ12#23512;3:50.1157809110629:7.93834897779404e-06:0.000223289315618592
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}}
}}

Revision as of 14:19, 5 September 2012


Full id: C4611_smallcell_neuroblastoma_colon_occipital_acute_mesothelioma_maxillary



Phase1 CAGE Peaks

Hg19::chr6:48036363..48036404,-p4@C6orf138
Hg19::chr6:48036553..48036578,-p3@C6orf138
Hg19::chr6:48036820..48036832,-p6@C6orf138


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 tube8.09e-4257
neural rod8.09e-4257
future spinal cord8.09e-4257
neural keel8.09e-4257
regional part of nervous system9.67e-3994
nervous system9.67e-3994
central nervous system2.83e-3682
neural plate8.44e-3686
presumptive neural plate8.44e-3686
brain2.14e-3469
future brain2.14e-3469
regional part of brain2.99e-3459
neurectoderm2.61e-3390
cerebral hemisphere1.42e-3232
regional part of forebrain3.71e-3241
forebrain3.71e-3241
future forebrain3.71e-3241
gray matter3.82e-3234
brain grey matter3.82e-3234
telencephalon5.54e-3234
anterior neural tube4.28e-3142
regional part of telencephalon9.84e-3133
neocortex1.30e-2720
pre-chordal neural plate2.61e-2761
regional part of cerebral cortex5.45e-2722
cerebral cortex1.02e-2425
pallium1.02e-2425
ectoderm-derived structure6.26e-24169
ectoderm7.99e-23173
presumptive ectoderm7.99e-23173
head5.61e-21123
anterior region of body3.99e-19129
craniocervical region3.99e-19129
adult organism3.28e-17115
organ part1.50e-12219
posterior neural tube1.36e-1115
chordal neural plate1.36e-1115
temporal lobe3.49e-117
basal ganglion3.86e-099
nuclear complex of neuraxis3.86e-099
aggregate regional part of brain3.86e-099
collection of basal ganglia3.86e-099
cerebral subcortex3.86e-099
gyrus4.56e-096
segmental subdivision of hindbrain6.67e-0912
hindbrain6.67e-0912
presumptive hindbrain6.67e-0912
nucleus of brain8.04e-099
neural nucleus8.04e-099
segmental subdivision of nervous system5.12e-0813
occipital lobe6.08e-085
parietal lobe7.97e-085
epithelium2.54e-07309
tube2.78e-07194
cell layer4.63e-07312
telencephalic nucleus8.86e-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
SUZ12#23512350.11578091106297.93834897779404e-060.000223289315618592



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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