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Coexpression cluster:C4663: Difference between revisions

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|ontology_enrichment_celltype=
|ontology_enrichment_celltype=
|ontology_enrichment_disease=
|ontology_enrichment_disease=
|ontology_enrichment_uberon=UBERON:0007023!8.40e-28!115;UBERON:0002780!1.47e-14!41;UBERON:0001890!1.47e-14!41;UBERON:0006240!1.47e-14!41;UBERON:0003080!1.52e-14!42;UBERON:0001017!2.12e-14!82;UBERON:0001893!4.85e-14!34;UBERON:0001869!5.17e-14!32;UBERON:0005743!5.61e-14!86;UBERON:0002616!9.77e-14!59;UBERON:0003075!1.05e-13!86;UBERON:0007284!1.05e-13!86;UBERON:0003056!1.29e-13!61;UBERON:0002020!1.38e-13!34;UBERON:0003528!1.38e-13!34;UBERON:0001049!1.69e-13!57;UBERON:0005068!1.69e-13!57;UBERON:0006241!1.69e-13!57;UBERON:0007135!1.69e-13!57;UBERON:0002791!2.00e-13!33;UBERON:0002619!2.07e-13!22;UBERON:0001950!3.99e-13!20;UBERON:0000153!1.27e-12!129;UBERON:0007811!1.27e-12!129;UBERON:0000955!1.11e-11!69;UBERON:0006238!1.11e-11!69;UBERON:0002346!1.29e-11!90;UBERON:0000956!1.31e-11!25;UBERON:0000203!1.31e-11!25;UBERON:0000033!2.02e-11!123;UBERON:0000073!2.22e-10!94;UBERON:0001016!2.22e-10!94;UBERON:0004121!1.98e-08!169;UBERON:0000924!2.29e-07!173;UBERON:0006601!2.29e-07!173
|ontology_enrichment_uberon=UBERON:0001950!1.52e-24!20;UBERON:0001893!8.63e-23!34;UBERON:0001869!9.10e-23!32;UBERON:0003528!1.48e-22!34;UBERON:0002020!1.48e-22!34;UBERON:0002791!2.20e-22!32;UBERON:0002619!7.53e-22!22;UBERON:0007023!1.16e-21!114;UBERON:0002780!4.05e-21!41;UBERON:0001890!4.05e-21!41;UBERON:0003080!4.05e-21!41;UBERON:0006240!4.05e-21!41;UBERON:0001017!9.71e-20!81;UBERON:0000956!1.34e-18!25;UBERON:0000203!1.34e-18!25;UBERON:0000073!2.69e-18!53;UBERON:0002616!2.69e-18!53;UBERON:0001049!7.81e-17!56;UBERON:0005068!7.81e-17!56;UBERON:0006241!7.81e-17!56;UBERON:0007135!7.81e-17!56;UBERON:0001016!1.39e-16!89;UBERON:0000955!1.93e-16!68;UBERON:0006238!1.93e-16!68;UBERON:0003056!6.09e-16!61;UBERON:0003075!6.48e-14!82;UBERON:0007284!6.48e-14!82;UBERON:0004121!7.50e-14!171;UBERON:0000924!7.50e-14!171;UBERON:0006601!7.50e-14!171;UBERON:0002346!8.53e-13!86;UBERON:0010371!1.43e-11!104;UBERON:0000200!1.69e-10!6;UBERON:0010314!9.25e-10!132;UBERON:0002021!6.27e-09!5;UBERON:0011216!1.71e-08!223;UBERON:0001871!6.89e-08!6;UBERON:0002420!1.53e-07!9;UBERON:0007245!1.53e-07!9;UBERON:0010009!1.53e-07!9;UBERON:0010011!1.53e-07!9;UBERON:0000454!1.53e-07!9
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}}
}}

Revision as of 16:08, 19 October 2012


Full id: C4663_meningioma_acute_Hair_Mesenchymal_immature_postcentral_occipital



Phase1 CAGE Peaks

Hg19::chr7:142552823..142552902,+p1@EPHB6
Hg19::chr7:142563227..142563251,+p@chr7:142563227..142563251
+
Hg19::chr7:142563953..142563963,+p@chr7:142563953..142563963
+


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
neocortex1.52e-2420
telencephalon8.63e-2334
cerebral hemisphere9.10e-2332
brain grey matter1.48e-2234
gray matter1.48e-2234
regional part of telencephalon2.20e-2232
regional part of cerebral cortex7.53e-2222
adult organism1.16e-21114
regional part of forebrain4.05e-2141
forebrain4.05e-2141
anterior neural tube4.05e-2141
future forebrain4.05e-2141
central nervous system9.71e-2081
cerebral cortex1.34e-1825
pallium1.34e-1825
regional part of nervous system2.69e-1853
regional part of brain2.69e-1853
neural tube7.81e-1756
neural rod7.81e-1756
future spinal cord7.81e-1756
neural keel7.81e-1756
nervous system1.39e-1689
brain1.93e-1668
future brain1.93e-1668
pre-chordal neural plate6.09e-1661
neural plate6.48e-1482
presumptive neural plate6.48e-1482
ectoderm-derived structure7.50e-14171
ectoderm7.50e-14171
presumptive ectoderm7.50e-14171
neurectoderm8.53e-1386
ecto-epithelium1.43e-11104
gyrus1.69e-106
structure with developmental contribution from neural crest9.25e-10132
occipital lobe6.27e-095
organ system subdivision1.71e-08223
temporal lobe6.89e-086
basal ganglion1.53e-079
nuclear complex of neuraxis1.53e-079
aggregate regional part of brain1.53e-079
collection of basal ganglia1.53e-079
cerebral subcortex1.53e-079


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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