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Coexpression cluster:C2723: Difference between revisions

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}}
}}

Revision as of 15:40, 26 November 2012


Full id: C2723_Pericytes_Meningeal_Smooth_Fibroblast_cerebellum_Hair_rhabdomyosarcoma



Phase1 CAGE Peaks

Hg19::chr3:147111231..147111281,+p3@ZIC1
Hg19::chr3:147111285..147111298,+p10@ZIC1
Hg19::chr3:147111317..147111328,+p8@ZIC1
Hg19::chr3:147131775..147131783,+p@chr3:147131775..147131783
+


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>

Uber Anatomy
Ontology termp-valuen
central nervous system2.88e-5281
nervous system9.93e-5289
brain1.61e-4868
future brain1.61e-4868
neural tube8.49e-4056
neural rod8.49e-4056
future spinal cord8.49e-4056
neural keel8.49e-4056
regional part of nervous system1.36e-3653
regional part of brain1.36e-3653
neural plate5.71e-3282
presumptive neural plate5.71e-3282
neurectoderm1.28e-2986
ecto-epithelium1.39e-28104
ectoderm-derived structure1.82e-28171
ectoderm1.82e-28171
presumptive ectoderm1.82e-28171
regional part of forebrain9.51e-2441
forebrain9.51e-2441
anterior neural tube9.51e-2441
future forebrain9.51e-2441
structure with developmental contribution from neural crest8.95e-22132
pre-chordal neural plate2.00e-2161
telencephalon4.72e-1934
brain grey matter1.03e-1834
gray matter1.03e-1834
posterior neural tube5.01e-1815
chordal neural plate5.01e-1815
cerebral hemisphere2.88e-1732
regional part of telencephalon3.41e-1732
organ system subdivision5.56e-15223
segmental subdivision of hindbrain7.18e-1512
hindbrain7.18e-1512
presumptive hindbrain7.18e-1512
segmental subdivision of nervous system1.99e-1313
cerebral cortex5.45e-1325
pallium5.45e-1325
regional part of metencephalon1.25e-119
metencephalon1.25e-119
future metencephalon1.25e-119
regional part of cerebral cortex5.50e-1122
adult organism3.73e-10114
vasculature of organ4.27e-1011
cell layer1.73e-09309
neocortex1.80e-0920
skin of body2.70e-0941
cerebellum3.23e-096
rhombic lip3.23e-096
epithelium3.25e-08306
brain vasculature5.48e-085
articulation8.61e-088
skeletal joint8.61e-088
articular system8.61e-088
intervertebral cartilage1.22e-075
symphysis1.22e-075
nonsynovial joint1.22e-075
fibrous joint1.22e-075
cartilaginous joint1.22e-075
developing mesenchymal condensation1.22e-075
pre-cartilage condensation1.22e-075
cartilaginous condensation1.22e-075
cartilage element1.22e-075
post-cranial axial skeletal system1.22e-075
vertebral column1.22e-075
intervertebral disk1.22e-075
intervertebral joint1.22e-075
integument1.32e-0746
integumental system1.32e-0746
brainstem2.36e-076
neural nucleus2.53e-079
nucleus of brain2.53e-079
Disease
Ontology termp-valuen
musculoskeletal system disease4.19e-075
myotonic disease4.19e-075
muscle tissue disease4.19e-075
myopathy4.19e-075
muscular disease4.19e-075
myotonic dystrophy4.19e-075


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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