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Coexpression cluster:C2950: Difference between revisions

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|ontology_enrichment_uberon=UBERON:0001017!9.58e-20!81;UBERON:0001049!1.68e-19!56;UBERON:0005068!1.68e-19!56;UBERON:0006241!1.68e-19!56;UBERON:0007135!1.68e-19!56;UBERON:0000073!3.42e-18!53;UBERON:0002616!3.42e-18!53;UBERON:0001016!2.42e-17!89;UBERON:0000955!4.45e-15!68;UBERON:0006238!4.45e-15!68;UBERON:0003075!6.26e-14!82;UBERON:0007284!6.26e-14!82;UBERON:0003528!1.46e-13!34;UBERON:0002020!1.46e-13!34;UBERON:0002780!2.34e-13!41;UBERON:0001890!2.34e-13!41;UBERON:0003080!2.34e-13!41;UBERON:0006240!2.34e-13!41;UBERON:0002346!4.18e-13!86;UBERON:0007023!5.18e-13!114;UBERON:0002298!1.89e-12!6;UBERON:0002791!6.85e-12!32;UBERON:0001869!6.85e-12!32;UBERON:0010371!1.65e-11!104;UBERON:0000007!3.30e-11!2;UBERON:0001893!4.15e-11!34;UBERON:0002771!4.63e-10!2;UBERON:0000956!6.52e-10!25;UBERON:0000203!6.52e-10!25;UBERON:0003056!7.00e-10!61;UBERON:0004121!7.59e-09!171;UBERON:0000924!7.59e-09!171;UBERON:0006601!7.59e-09!171;UBERON:0000349!9.22e-09!5;UBERON:0002619!9.65e-09!22;UBERON:0003076!1.56e-07!15;UBERON:0003057!1.56e-07!15;UBERON:0010314!3.08e-07!132;UBERON:0001950!3.40e-07!20;UBERON:0011216!3.54e-07!223;UBERON:0001896!4.21e-07!3;UBERON:0005290!4.21e-07!3;UBERON:0010096!4.21e-07!3;UBERON:0000988!5.38e-07!3;UBERON:0003135!7.47e-07!11
|ontology_enrichment_uberon=UBERON:0001017!9.58e-20!81;UBERON:0001049!1.68e-19!56;UBERON:0005068!1.68e-19!56;UBERON:0006241!1.68e-19!56;UBERON:0007135!1.68e-19!56;UBERON:0000073!3.42e-18!53;UBERON:0002616!3.42e-18!53;UBERON:0001016!2.42e-17!89;UBERON:0000955!4.45e-15!68;UBERON:0006238!4.45e-15!68;UBERON:0003075!6.26e-14!82;UBERON:0007284!6.26e-14!82;UBERON:0003528!1.46e-13!34;UBERON:0002020!1.46e-13!34;UBERON:0002780!2.34e-13!41;UBERON:0001890!2.34e-13!41;UBERON:0003080!2.34e-13!41;UBERON:0006240!2.34e-13!41;UBERON:0002346!4.18e-13!86;UBERON:0007023!5.18e-13!114;UBERON:0002298!1.89e-12!6;UBERON:0002791!6.85e-12!32;UBERON:0001869!6.85e-12!32;UBERON:0010371!1.65e-11!104;UBERON:0000007!3.30e-11!2;UBERON:0001893!4.15e-11!34;UBERON:0002771!4.63e-10!2;UBERON:0000956!6.52e-10!25;UBERON:0000203!6.52e-10!25;UBERON:0003056!7.00e-10!61;UBERON:0004121!7.59e-09!171;UBERON:0000924!7.59e-09!171;UBERON:0006601!7.59e-09!171;UBERON:0000349!9.22e-09!5;UBERON:0002619!9.65e-09!22;UBERON:0003076!1.56e-07!15;UBERON:0003057!1.56e-07!15;UBERON:0010314!3.08e-07!132;UBERON:0001950!3.40e-07!20;UBERON:0011216!3.54e-07!223;UBERON:0001896!4.21e-07!3;UBERON:0005290!4.21e-07!3;UBERON:0010096!4.21e-07!3;UBERON:0000988!5.38e-07!3;UBERON:0003135!7.47e-07!11
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}}
}}

Revision as of 15:50, 26 November 2012


Full id: C2950_embryonic_anaplastic_pituitary_small_thymus_H9_mycosis



Phase1 CAGE Peaks

Hg19::chrX:107976736..107976739,-p@chrX:107976736..107976739
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Hg19::chrX:107976961..107976965,-p@chrX:107976961..107976965
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Hg19::chrX:107979550..107979574,-p1@IRS4
Hg19::chrX:107979616..107979623,-p3@IRS4


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><br>

Cell Type
Ontology termp-valuen
embryonic stem cell8.39e-255
neuron7.68e-086
neuroblast7.68e-086
electrically signaling cell7.68e-086
Uber Anatomy
Ontology termp-valuen
central nervous system9.58e-2081
neural tube1.68e-1956
neural rod1.68e-1956
future spinal cord1.68e-1956
neural keel1.68e-1956
regional part of nervous system3.42e-1853
regional part of brain3.42e-1853
nervous system2.42e-1789
brain4.45e-1568
future brain4.45e-1568
neural plate6.26e-1482
presumptive neural plate6.26e-1482
brain grey matter1.46e-1334
gray matter1.46e-1334
regional part of forebrain2.34e-1341
forebrain2.34e-1341
anterior neural tube2.34e-1341
future forebrain2.34e-1341
neurectoderm4.18e-1386
adult organism5.18e-13114
brainstem1.89e-126
regional part of telencephalon6.85e-1232
cerebral hemisphere6.85e-1232
ecto-epithelium1.65e-11104
pituitary gland3.30e-112
telencephalon4.15e-1134
middle temporal gyrus4.63e-102
cerebral cortex6.52e-1025
pallium6.52e-1025
pre-chordal neural plate7.00e-1061
ectoderm-derived structure7.59e-09171
ectoderm7.59e-09171
presumptive ectoderm7.59e-09171
limbic system9.22e-095
regional part of cerebral cortex9.65e-0922
posterior neural tube1.56e-0715
chordal neural plate1.56e-0715
structure with developmental contribution from neural crest3.08e-07132
neocortex3.40e-0720
organ system subdivision3.54e-07223
medulla oblongata4.21e-073
myelencephalon4.21e-073
future myelencephalon4.21e-073
pons5.38e-073
male reproductive organ7.47e-0711


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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