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Coexpression cluster:C2635: Difference between revisions

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|ontology_enrichment_celltype=
|ontology_enrichment_celltype=
|ontology_enrichment_disease=
|ontology_enrichment_disease=
|ontology_enrichment_uberon=UBERON:0001049!6.71e-32!57;UBERON:0005068!6.71e-32!57;UBERON:0006241!6.71e-32!57;UBERON:0007135!6.71e-32!57;UBERON:0007023!4.12e-31!115;UBERON:0005743!2.43e-29!86;UBERON:0001017!3.76e-29!82;UBERON:0000073!1.18e-27!94;UBERON:0001016!1.18e-27!94;UBERON:0002346!2.43e-27!90;UBERON:0003075!2.80e-26!86;UBERON:0007284!2.80e-26!86;UBERON:0003080!4.53e-26!42;UBERON:0002780!8.80e-26!41;UBERON:0001890!8.80e-26!41;UBERON:0006240!8.80e-26!41;UBERON:0002616!5.83e-25!59;UBERON:0000955!5.86e-24!69;UBERON:0006238!5.86e-24!69;UBERON:0002020!2.17e-23!34;UBERON:0003528!2.17e-23!34;UBERON:0001893!5.95e-23!34;UBERON:0002791!1.26e-22!33;UBERON:0001869!1.73e-21!32;UBERON:0003056!4.04e-20!61;UBERON:0000956!4.67e-17!25;UBERON:0000203!4.67e-17!25;UBERON:0002619!8.62e-16!22;UBERON:0000924!1.65e-14!173;UBERON:0006601!1.65e-14!173;UBERON:0001950!2.87e-14!20;UBERON:0000153!1.03e-13!129;UBERON:0007811!1.03e-13!129;UBERON:0004121!1.26e-13!169;UBERON:0000033!5.02e-13!123;UBERON:0002420!6.61e-08!9;UBERON:0007245!6.61e-08!9;UBERON:0010009!6.61e-08!9;UBERON:0010011!6.61e-08!9;UBERON:0000454!6.61e-08!9;UBERON:0002308!8.41e-08!9;UBERON:0000125!8.41e-08!9;UBERON:0003076!3.88e-07!15;UBERON:0003057!3.88e-07!15;UBERON:0001871!8.63e-07!7;UBERON:0002298!9.41e-07!8
|ontology_enrichment_uberon=UBERON:0001049!2.60e-37!56;UBERON:0005068!2.60e-37!56;UBERON:0006241!2.60e-37!56;UBERON:0007135!2.60e-37!56;UBERON:0000073!2.78e-34!53;UBERON:0002616!2.78e-34!53;UBERON:0001017!5.08e-32!81;UBERON:0002780!4.25e-31!41;UBERON:0001890!4.25e-31!41;UBERON:0003080!4.25e-31!41;UBERON:0006240!4.25e-31!41;UBERON:0002346!2.70e-30!86;UBERON:0001016!4.19e-30!89;UBERON:0007023!4.29e-30!114;UBERON:0003075!9.89e-29!82;UBERON:0007284!9.89e-29!82;UBERON:0003528!1.05e-27!34;UBERON:0002020!1.05e-27!34;UBERON:0001893!3.34e-27!34;UBERON:0000955!5.66e-27!68;UBERON:0006238!5.66e-27!68;UBERON:0002791!4.86e-26!32;UBERON:0001869!1.40e-25!32;UBERON:0003056!3.21e-23!61;UBERON:0011216!3.94e-20!223;UBERON:0010371!5.97e-20!104;UBERON:0000956!6.45e-20!25;UBERON:0000203!6.45e-20!25;UBERON:0002619!3.33e-18!22;UBERON:0001950!2.74e-16!20;UBERON:0010314!5.74e-15!132;UBERON:0004121!3.62e-14!171;UBERON:0000924!3.62e-14!171;UBERON:0006601!3.62e-14!171;UBERON:0000477!2.89e-10!373;UBERON:0002420!1.69e-09!9;UBERON:0007245!1.69e-09!9;UBERON:0010009!1.69e-09!9;UBERON:0010011!1.69e-09!9;UBERON:0000454!1.69e-09!9;UBERON:0000125!3.00e-09!9;UBERON:0002308!3.00e-09!9;UBERON:0003076!1.19e-07!15;UBERON:0003057!1.19e-07!15;UBERON:0009663!1.23e-07!7;UBERON:0000481!1.69e-07!342;UBERON:0001871!3.42e-07!6;UBERON:0003101!9.41e-07!22;UBERON:0000079!9.41e-07!22;UBERON:0002298!9.55e-07!6
|tf_chipseq_enrich=BCL3#602;3:25.9103271028037:9.48553136097325e-05:0.00137438874834723
|tf_chipseq_enrich=BCL3#602;3:25.9103271028037:9.48553136097325e-05:0.00137438874834723
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}}
}}

Revision as of 14:15, 19 October 2012


Full id: C2635_cerebellum_parietal_retinoblastoma_acute_temporal_occipital_thalamus



Phase1 CAGE Peaks

Hg19::chr21:44082526..44082558,+p3@PDE9A
Hg19::chr21:44090044..44090062,+p@chr21:44090044..44090062
+
Hg19::chr21:44090097..44090110,+p@chr21:44090097..44090110
+
Hg19::chr21:44090232..44090251,+p@chr21:44090232..44090251
+


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 tube2.60e-3756
neural rod2.60e-3756
future spinal cord2.60e-3756
neural keel2.60e-3756
regional part of nervous system2.78e-3453
regional part of brain2.78e-3453
central nervous system5.08e-3281
regional part of forebrain4.25e-3141
forebrain4.25e-3141
anterior neural tube4.25e-3141
future forebrain4.25e-3141
neurectoderm2.70e-3086
nervous system4.19e-3089
adult organism4.29e-30114
neural plate9.89e-2982
presumptive neural plate9.89e-2982
brain grey matter1.05e-2734
gray matter1.05e-2734
telencephalon3.34e-2734
brain5.66e-2768
future brain5.66e-2768
regional part of telencephalon4.86e-2632
cerebral hemisphere1.40e-2532
pre-chordal neural plate3.21e-2361
organ system subdivision3.94e-20223
ecto-epithelium5.97e-20104
cerebral cortex6.45e-2025
pallium6.45e-2025
regional part of cerebral cortex3.33e-1822
neocortex2.74e-1620
structure with developmental contribution from neural crest5.74e-15132
ectoderm-derived structure3.62e-14171
ectoderm3.62e-14171
presumptive ectoderm3.62e-14171
anatomical cluster2.89e-10373
basal ganglion1.69e-099
nuclear complex of neuraxis1.69e-099
aggregate regional part of brain1.69e-099
collection of basal ganglia1.69e-099
cerebral subcortex1.69e-099
neural nucleus3.00e-099
nucleus of brain3.00e-099
posterior neural tube1.19e-0715
chordal neural plate1.19e-0715
telencephalic nucleus1.23e-077
multi-tissue structure1.69e-07342
temporal lobe3.42e-076
male organism9.41e-0722
male reproductive system9.41e-0722
brainstem9.55e-076


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
BCL3#602325.91032710280379.48553136097325e-050.00137438874834723



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:C2635&oldid=2248774"