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Coexpression cluster:C2070: Difference between revisions

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|ontology_enrichment_uberon=UBERON:0007023!5.89e-36!114;UBERON:0001869!2.39e-14!32;UBERON:0002780!2.39e-13!41;UBERON:0001890!2.39e-13!41;UBERON:0003080!2.39e-13!41;UBERON:0006240!2.39e-13!41;UBERON:0003528!2.86e-13!34;UBERON:0002020!2.86e-13!34;UBERON:0002791!3.69e-13!32;UBERON:0002619!3.69e-13!22;UBERON:0001893!4.32e-13!34;UBERON:0001049!1.06e-12!56;UBERON:0005068!1.06e-12!56;UBERON:0006241!1.06e-12!56;UBERON:0007135!1.06e-12!56;UBERON:0002346!1.12e-12!86;UBERON:0000073!5.22e-12!53;UBERON:0002616!5.22e-12!53;UBERON:0001950!2.11e-11!20;UBERON:0000956!5.58e-11!25;UBERON:0000203!5.58e-11!25;UBERON:0001016!8.90e-11!89;UBERON:0003075!3.12e-10!82;UBERON:0007284!3.12e-10!82;UBERON:0001017!8.46e-10!81;UBERON:0004121!2.59e-09!171;UBERON:0000924!2.59e-09!171;UBERON:0006601!2.59e-09!171;UBERON:0003056!3.18e-09!61;UBERON:0010371!6.46e-09!104;UBERON:0000955!1.17e-08!68;UBERON:0006238!1.17e-08!68;UBERON:0010314!6.78e-08!132
|ontology_enrichment_uberon=UBERON:0007023!5.89e-36!114;UBERON:0001869!2.39e-14!32;UBERON:0002780!2.39e-13!41;UBERON:0001890!2.39e-13!41;UBERON:0003080!2.39e-13!41;UBERON:0006240!2.39e-13!41;UBERON:0003528!2.86e-13!34;UBERON:0002020!2.86e-13!34;UBERON:0002791!3.69e-13!32;UBERON:0002619!3.69e-13!22;UBERON:0001893!4.32e-13!34;UBERON:0001049!1.06e-12!56;UBERON:0005068!1.06e-12!56;UBERON:0006241!1.06e-12!56;UBERON:0007135!1.06e-12!56;UBERON:0002346!1.12e-12!86;UBERON:0000073!5.22e-12!53;UBERON:0002616!5.22e-12!53;UBERON:0001950!2.11e-11!20;UBERON:0000956!5.58e-11!25;UBERON:0000203!5.58e-11!25;UBERON:0001016!8.90e-11!89;UBERON:0003075!3.12e-10!82;UBERON:0007284!3.12e-10!82;UBERON:0001017!8.46e-10!81;UBERON:0004121!2.59e-09!171;UBERON:0000924!2.59e-09!171;UBERON:0006601!2.59e-09!171;UBERON:0003056!3.18e-09!61;UBERON:0010371!6.46e-09!104;UBERON:0000955!1.17e-08!68;UBERON:0006238!1.17e-08!68;UBERON:0010314!6.78e-08!132
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}}
}}

Revision as of 15:16, 26 November 2012


Full id: C2070_testis_skeletal_diaphragm_left_throat_cord_tongue



Phase1 CAGE Peaks

Hg19::chr10:72141330..72141337,-p12@LRRC20
Hg19::chr1:167906109..167906124,+p2@DCAF6
Hg19::chr22:18593507..18593556,+p3@TUBA8
Hg19::chr2:79006881..79006887,+p@chr2:79006881..79006887
+


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
adult organism5.89e-36114
cerebral hemisphere2.39e-1432
regional part of forebrain2.39e-1341
forebrain2.39e-1341
anterior neural tube2.39e-1341
future forebrain2.39e-1341
brain grey matter2.86e-1334
gray matter2.86e-1334
regional part of telencephalon3.69e-1332
regional part of cerebral cortex3.69e-1322
telencephalon4.32e-1334
neural tube1.06e-1256
neural rod1.06e-1256
future spinal cord1.06e-1256
neural keel1.06e-1256
neurectoderm1.12e-1286
regional part of nervous system5.22e-1253
regional part of brain5.22e-1253
neocortex2.11e-1120
cerebral cortex5.58e-1125
pallium5.58e-1125
nervous system8.90e-1189
neural plate3.12e-1082
presumptive neural plate3.12e-1082
central nervous system8.46e-1081
ectoderm-derived structure2.59e-09171
ectoderm2.59e-09171
presumptive ectoderm2.59e-09171
pre-chordal neural plate3.18e-0961
ecto-epithelium6.46e-09104
brain1.17e-0868
future brain1.17e-0868
structure with developmental contribution from neural crest6.78e-08132
Disease
Ontology termp-valuen
neuroectodermal tumor2.76e-0710


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)

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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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