Personal tools

Coexpression cluster:C789

From FANTOM5_SSTAR

Revision as of 09:30, 12 September 2012 by Autoedit (talk | contribs)
Jump to: navigation, search


Full id: C789_retina_Retinal_medulla_stomach_lung_eye_corpus



Phase1 CAGE Peaks

  Short description
Hg19::chr11:109990513..109990520,- p@chr11:109990513..109990520
-
Hg19::chr11:61522820..61522823,+ p9@C11orf9
Hg19::chr11:61522844..61522875,+ p2@C11orf9
Hg19::chr13:99135322..99135327,- p@chr13:99135322..99135327
-
Hg19::chr14:87636652..87636657,- p@chr14:87636652..87636657
-
Hg19::chr21:36041264..36041274,+ p3@CLIC6
Hg19::chr21:36041275..36041282,+ p5@CLIC6
Hg19::chr21:36041286..36041333,+ p1@CLIC6
Hg19::chr5:70308745..70308754,- p@chr5:70308745..70308754
-
Hg19::chr9:140088882..140088898,- p@chr9:140088882..140088898
-


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


GO IDGO nameFDR corrected p-value
GO:0005247voltage-gated chloride channel activity0.0445095728958841
GO:0022844voltage-gated anion channel activity0.0445095728958841
GO:0043168anion binding0.0445095728958841
GO:0031404chloride ion binding0.0445095728958841
GO:0005254chloride channel activity0.0445095728958841
GO:0006821chloride transport0.0445095728958841
GO:0005253anion channel activity0.0445095728958841



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


uberon_data


Uber Anatomy
Ontology termp-valuen
adult organism1.03e-53115
neural plate7.47e-2786
presumptive neural plate7.47e-2786
central nervous system1.08e-2482
neurectoderm1.29e-2490
regional part of nervous system1.62e-2494
nervous system1.62e-2494
neural tube5.61e-2357
neural rod5.61e-2357
future spinal cord5.61e-2357
neural keel5.61e-2357
brain1.47e-2269
future brain1.47e-2269
regional part of brain9.72e-2259
anterior region of body6.69e-20129
craniocervical region6.69e-20129
pre-chordal neural plate1.82e-1961
head3.67e-18123
anterior neural tube2.84e-1742
regional part of forebrain1.51e-1641
forebrain1.51e-1641
future forebrain1.51e-1641
ectoderm-derived structure4.46e-15169
ectoderm3.88e-14173
presumptive ectoderm3.88e-14173
telencephalon1.46e-1234
gray matter1.64e-1234
brain grey matter1.64e-1234
regional part of telencephalon4.83e-1233
cerebral hemisphere5.17e-1132
regional part of cerebral cortex1.70e-1022
neocortex3.05e-0920
cerebral cortex1.51e-0825
pallium1.51e-0825
brainstem1.92e-088
organism subdivision7.16e-08365
organ part1.11e-07219
organ1.83e-07511
segmental subdivision of nervous system4.27e-0713
posterior neural tube6.32e-0715
chordal neural plate6.32e-0715


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


No analysis results for this cluster

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.