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{{Coexpression_clusters
 
{{Coexpression_clusters
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|full_id=C2624_argyrophil_breast_bronchogenic_small_transitionalcell_epidermoid_gall
 
|full_id=C2624_argyrophil_breast_bronchogenic_small_transitionalcell_epidermoid_gall
 
|id=C2624
 
|id=C2624

Revision as of 06:23, 12 September 2012


Full id: C2624_argyrophil_breast_bronchogenic_small_transitionalcell_epidermoid_gall



Phase1 CAGE Peaks

  Short description
Hg19::chr20:58497478..58497482,- p6@SYCP2
Hg19::chr20:58508359..58508420,- p2@SYCP2
Hg19::chr20:58508665..58508672,- p5@SYCP2
Hg19::chr20:58508681..58508698,- p1@SYCP2


Enriched pathways on this co-expression clusterSummary:
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.
Analyst: Emmanuel Dimont

link to source dataset
data


No results for this coexpression

Enriched Gene Ontology terms on this co-expression clusterSummary: 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.
Analyst: Erik Arner

link to source dataset
data


No GOStat results

Enriched sample ontology terms on this co-expression clusterSummary: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. Analyst: Hideya Kawaji

links to source dataset

cell_data
uberon_data


Cell Type
Ontology termp-valuen
mature alpha-beta T cell2.91e-0818
alpha-beta T cell2.91e-0818
immature T cell2.91e-0818
mature T cell2.91e-0818
immature alpha-beta T cell2.91e-0818
Uber Anatomy
Ontology termp-valuen
adult organism5.07e-17115
neural tube2.83e-1257
neural rod2.83e-1257
future spinal cord2.83e-1257
neural keel2.83e-1257
gray matter1.80e-1134
brain grey matter1.80e-1134
telencephalon1.84e-1134
cerebral hemisphere3.77e-1132
anterior neural tube6.48e-1142
regional part of telencephalon6.95e-1133
regional part of forebrain1.34e-1041
forebrain1.34e-1041
future forebrain1.34e-1041
neocortex6.72e-1020
cerebral cortex1.01e-0925
pallium1.01e-0925
regional part of brain1.13e-0959
regional part of cerebral cortex2.50e-0922
neural plate3.25e-0986
presumptive neural plate3.25e-0986
neurectoderm4.28e-0890
brain2.27e-0769
future brain2.27e-0769
central nervous system3.08e-0782
pre-chordal neural plate3.98e-0761


Overrepresented TFBS (DNA) motifs on this co-expression clusterSummary: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. Analyst: Michiel de Hoon

link to source data
Novel motifs
data

Jaspar motifs
data


Novel motifs



JASPAR motifs

Motifs-log10(p-value)

{{{tfbs_overrepresentation_jaspar}}}



ENCODE TF ChIP-seq peak enrichment analysisSummary: 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.
Analyst: Erik Arner

link to source dataset

data


(#promoters = Number of promoters in this coexpression cluster that have ChIP signal of the TF)

TF#promotersEnrichmentp-valueq-value
FOS#235336.74846648167080.005032452776317940.0234719692526737
NFYA#4800313.81918552487290.0006132411806734510.00508869344258339
NFYB#4801312.56984494015230.000811456397697350.00619048171797762
SP2#6668319.61514787038350.0002171004269245340.00248670229080625



Relative expression of the co-expression clusterSummary:Co-expression clusters are compared against FANTOM5 samples to obtain relative expression.
Analyst:NA

link to data source
data


This analysis result is provided for C0 - C305 clusters.