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Coexpression cluster:C4072: Difference between revisions

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{{Coexpression_clusters
{{Coexpression_clusters
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|full_id=C4072_occipital_seminal_olfactory_parietal_Hepatocyte_locus_medial
|full_id=C4072_occipital_seminal_olfactory_parietal_Hepatocyte_locus_medial
|id=C4072
|id=C4072

Revision as of 17:06, 12 September 2012


Full id: C4072_occipital_seminal_olfactory_parietal_Hepatocyte_locus_medial



Phase1 CAGE Peaks

Hg19::chr21:27394286..27394319,-p17@APP
Hg19::chr21:27394320..27394368,-p8@APP
Hg19::chr21:27423401..27423412,-p23@APP


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
epithelial cell2.60e-09254
embryonic cell7.08e-07248
Uber Anatomy
Ontology termp-valuen
neural tube5.86e-2357
neural rod5.86e-2357
future spinal cord5.86e-2357
neural keel5.86e-2357
central nervous system7.16e-2282
regional part of brain1.03e-2059
regional part of nervous system4.96e-2094
nervous system4.96e-2094
neurectoderm6.31e-2090
multi-cellular organism9.19e-20659
anterior neural tube1.11e-1942
regional part of forebrain2.04e-1941
forebrain2.04e-1941
future forebrain2.04e-1941
neural plate2.39e-1986
presumptive neural plate2.39e-1986
brain3.19e-1969
future brain3.19e-1969
ectoderm2.44e-18173
presumptive ectoderm2.44e-18173
ectoderm-derived structure1.09e-17169
gray matter1.63e-1734
brain grey matter1.63e-1734
head2.81e-17123
anatomical conduit3.29e-17241
adult organism4.56e-17115
telencephalon5.96e-1734
anatomical system1.23e-16625
regional part of telencephalon1.41e-1633
anatomical cluster1.47e-16286
anatomical group2.83e-16626
cerebral hemisphere3.39e-1632
pre-chordal neural plate4.31e-1661
anterior region of body9.80e-16129
craniocervical region9.80e-16129
embryo1.43e-15612
epithelium2.42e-14309
embryonic structure4.15e-14605
developing anatomical structure4.15e-14605
germ layer7.21e-14604
embryonic tissue7.21e-14604
presumptive structure7.21e-14604
epiblast (generic)7.21e-14604
cell layer1.02e-13312
regional part of cerebral cortex5.14e-1322
tube6.43e-13194
cerebral cortex6.51e-1325
pallium6.51e-1325
organism subdivision5.33e-12365
neocortex9.86e-1220
organ1.22e-11511
multi-tissue structure1.24e-10347
organ part1.95e-08219


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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