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{{Coexpression_clusters
{{Coexpression_clusters
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|full_id=C2549_Fibroblast_Lens_Astrocyte_heart_Ciliary_liposarcoma_Adipocyte
|full_id=C2549_Fibroblast_Lens_Astrocyte_heart_Ciliary_liposarcoma_Adipocyte
|id=C2549
|id=C2549

Revision as of 15:18, 12 September 2012


Full id: C2549_Fibroblast_Lens_Astrocyte_heart_Ciliary_liposarcoma_Adipocyte



Phase1 CAGE Peaks

Hg19::chr1:201708474..201708479,+p58@NAV1
Hg19::chr1:201708485..201708494,+p55@NAV1
Hg19::chr1:201708502..201708514,+p24@NAV1
Hg19::chr8:24997361..24997368,-p@chr8:24997361..24997368
-


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
cardiocyte3.65e-0716
Uber Anatomy
Ontology termp-valuen
primary circulatory organ2.79e-1327
neural plate6.51e-1186
presumptive neural plate6.51e-1186
vasculature of head1.23e-1011
vasculature of organ1.23e-1011
heart1.27e-1024
primitive heart tube1.27e-1024
primary heart field1.27e-1024
anterior lateral plate mesoderm1.27e-1024
heart tube1.27e-1024
heart primordium1.27e-1024
cardiac mesoderm1.27e-1024
cardiogenic plate1.27e-1024
heart rudiment1.27e-1024
neurectoderm1.38e-1090
circulatory system8.31e-10113
cell layer9.01e-10312
regional part of brain1.12e-0859
epithelium1.26e-08309
brain2.44e-0869
future brain2.44e-0869
cardiovascular system2.48e-08110
anterior region of body3.17e-08129
craniocervical region3.17e-08129
head3.30e-08123
central nervous system4.44e-0882
vasculature of eye7.71e-086
uvea7.71e-086
tube9.12e-08194
organism subdivision1.26e-07365
adult organism3.94e-07115
regional part of nervous system9.89e-0794
nervous system9.89e-0794


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.