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Coexpression cluster:C3934: Difference between revisions

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|ontology_enrichment_uberon=UBERON:0001049!3.06e-26!56;UBERON:0005068!3.06e-26!56;UBERON:0006241!3.06e-26!56;UBERON:0007135!3.06e-26!56;UBERON:0000073!5.46e-26!53;UBERON:0002616!5.46e-26!53;UBERON:0001893!4.35e-24!34;UBERON:0003528!6.97e-24!34;UBERON:0002020!6.97e-24!34;UBERON:0002780!2.53e-23!41;UBERON:0001890!2.53e-23!41;UBERON:0003080!2.53e-23!41;UBERON:0006240!2.53e-23!41;UBERON:0000955!3.90e-21!68;UBERON:0006238!3.90e-21!68;UBERON:0001869!5.70e-21!32;UBERON:0002791!7.19e-21!32;UBERON:0001017!2.00e-19!81;UBERON:0002346!4.31e-18!86;UBERON:0002619!1.36e-17!22;UBERON:0010371!5.25e-17!104;UBERON:0003075!1.24e-16!82;UBERON:0007284!1.24e-16!82;UBERON:0001016!1.24e-16!89;UBERON:0000956!4.12e-15!25;UBERON:0000203!4.12e-15!25;UBERON:0003056!5.21e-15!61;UBERON:0004121!1.89e-14!171;UBERON:0000924!1.89e-14!171;UBERON:0006601!1.89e-14!171;UBERON:0001950!2.09e-14!20;UBERON:0010314!2.02e-11!132;UBERON:0000349!2.76e-11!5;UBERON:0002420!5.49e-11!9;UBERON:0007245!5.49e-11!9;UBERON:0010009!5.49e-11!9;UBERON:0010011!5.49e-11!9;UBERON:0000454!5.49e-11!9;UBERON:0000125!9.18e-11!9;UBERON:0002308!9.18e-11!9;UBERON:0003343!1.08e-10!4;UBERON:0004785!1.08e-10!4;UBERON:0011216!1.35e-09!223;UBERON:0000200!1.97e-09!6;UBERON:0007023!5.20e-09!114;UBERON:0000064!1.18e-08!218;UBERON:0003729!3.91e-08!13;UBERON:0004111!7.37e-08!240;UBERON:0009663!1.84e-07!7;UBERON:0001870!2.17e-07!3
|ontology_enrichment_uberon=UBERON:0001049!3.06e-26!56;UBERON:0005068!3.06e-26!56;UBERON:0006241!3.06e-26!56;UBERON:0007135!3.06e-26!56;UBERON:0000073!5.46e-26!53;UBERON:0002616!5.46e-26!53;UBERON:0001893!4.35e-24!34;UBERON:0003528!6.97e-24!34;UBERON:0002020!6.97e-24!34;UBERON:0002780!2.53e-23!41;UBERON:0001890!2.53e-23!41;UBERON:0003080!2.53e-23!41;UBERON:0006240!2.53e-23!41;UBERON:0000955!3.90e-21!68;UBERON:0006238!3.90e-21!68;UBERON:0001869!5.70e-21!32;UBERON:0002791!7.19e-21!32;UBERON:0001017!2.00e-19!81;UBERON:0002346!4.31e-18!86;UBERON:0002619!1.36e-17!22;UBERON:0010371!5.25e-17!104;UBERON:0003075!1.24e-16!82;UBERON:0007284!1.24e-16!82;UBERON:0001016!1.24e-16!89;UBERON:0000956!4.12e-15!25;UBERON:0000203!4.12e-15!25;UBERON:0003056!5.21e-15!61;UBERON:0004121!1.89e-14!171;UBERON:0000924!1.89e-14!171;UBERON:0006601!1.89e-14!171;UBERON:0001950!2.09e-14!20;UBERON:0010314!2.02e-11!132;UBERON:0000349!2.76e-11!5;UBERON:0002420!5.49e-11!9;UBERON:0007245!5.49e-11!9;UBERON:0010009!5.49e-11!9;UBERON:0010011!5.49e-11!9;UBERON:0000454!5.49e-11!9;UBERON:0000125!9.18e-11!9;UBERON:0002308!9.18e-11!9;UBERON:0003343!1.08e-10!4;UBERON:0004785!1.08e-10!4;UBERON:0011216!1.35e-09!223;UBERON:0000200!1.97e-09!6;UBERON:0007023!5.20e-09!114;UBERON:0000064!1.18e-08!218;UBERON:0003729!3.91e-08!13;UBERON:0004111!7.37e-08!240;UBERON:0009663!1.84e-07!7;UBERON:0001870!2.17e-07!3
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}}
}}

Revision as of 16:26, 26 November 2012


Full id: C3934_glassy_epidermoid_oral_ductal_malignant_squamous_acantholytic



Phase1 CAGE Peaks

Hg19::chr1:209944599..209944616,-p@chr1:209944599..209944616
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Hg19::chr1:209945462..209945477,-p@chr1:209945462..209945477
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Hg19::chr1:209945709..209945715,-p@chr1:209945709..209945715
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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>cell_data<br>uberon_data<br>disease_data<br>

Cell Type
Ontology termp-valuen
epithelial cell of alimentary canal7.79e-0820
endo-epithelial cell2.59e-0742
Uber Anatomy
Ontology termp-valuen
neural tube3.06e-2656
neural rod3.06e-2656
future spinal cord3.06e-2656
neural keel3.06e-2656
regional part of nervous system5.46e-2653
regional part of brain5.46e-2653
telencephalon4.35e-2434
brain grey matter6.97e-2434
gray matter6.97e-2434
regional part of forebrain2.53e-2341
forebrain2.53e-2341
anterior neural tube2.53e-2341
future forebrain2.53e-2341
brain3.90e-2168
future brain3.90e-2168
cerebral hemisphere5.70e-2132
regional part of telencephalon7.19e-2132
central nervous system2.00e-1981
neurectoderm4.31e-1886
regional part of cerebral cortex1.36e-1722
ecto-epithelium5.25e-17104
neural plate1.24e-1682
presumptive neural plate1.24e-1682
nervous system1.24e-1689
cerebral cortex4.12e-1525
pallium4.12e-1525
pre-chordal neural plate5.21e-1561
ectoderm-derived structure1.89e-14171
ectoderm1.89e-14171
presumptive ectoderm1.89e-14171
neocortex2.09e-1420
structure with developmental contribution from neural crest2.02e-11132
limbic system2.76e-115
basal ganglion5.49e-119
nuclear complex of neuraxis5.49e-119
aggregate regional part of brain5.49e-119
collection of basal ganglia5.49e-119
cerebral subcortex5.49e-119
neural nucleus9.18e-119
nucleus of brain9.18e-119
mucosa of oral region1.08e-104
respiratory system mucosa1.08e-104
organ system subdivision1.35e-09223
gyrus1.97e-096
adult organism5.20e-09114
organ part1.18e-08218
mouth mucosa3.91e-0813
anatomical conduit7.37e-08240
telencephalic nucleus1.84e-077
frontal cortex2.17e-073
Disease
Ontology termp-valuen
squamous cell carcinoma3.32e-2314
carcinoma5.34e-12106
cell type cancer5.77e-09143


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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