Personal tools

Coexpression cluster:C1202

From FANTOM5_SSTAR

Revision as of 14:08, 21 May 2012 by Autoedit (talk | contribs)
Jump to: navigation, search


Full id: C1202_hippocampus_amygdala_medial_middle_parietal_pons_insula



Phase1 CAGE Peaks

Hg19::chr14:70234642..70234664,+p17@SRSF5
Hg19::chr15:80733538..80733547,+p23@ARNT2
Hg19::chr5:153191119..153191132,+p11@GRIA1
Hg19::chr5:22754587..22754623,+p@chr5:22754587..22754623
+
Hg19::chr6:95445637..95445675,-p@chr6:95445637..95445675
-
Hg19::chrX:85218889..85218912,-p@chrX:85218889..85218912
-
Hg19::chrX:85218927..85218946,-p@chrX:85218927..85218946
-


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


GO IDGO nameFDR corrected p-value
GO:0017162aryl hydrocarbon receptor binding0.00718217406696926
GO:0005061aryl hydrocarbon receptor nuclear translocator activity0.00718217406696926
GO:0004971alpha-amino-3-hydroxy-5-methyl-4-isoxazole propionate selective glutamate receptor activity0.00718217406696926
GO:0015277kainate selective glutamate receptor activity0.0143632909991038
GO:0004970ionotropic glutamate receptor activity0.0448575345827884
GO:0005234extracellular-glutamate-gated ion channel activity0.0448575345827884
GO:0001666response to hypoxia0.0448575345827884
GO:0001701in utero embryonic development0.0448575345827884



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><br>uberon_data<br><br>


Uber Anatomy
Ontology termp-valuen
neural tube5.19e-2657
neural rod5.19e-2657
future spinal cord5.19e-2657
neural keel5.19e-2657
regional part of brain5.27e-2359
central nervous system6.07e-2382
regional part of forebrain5.06e-2241
forebrain5.06e-2241
future forebrain5.06e-2241
brain5.55e-2169
future brain5.55e-2169
anterior neural tube6.79e-2142
gray matter3.51e-2034
brain grey matter3.51e-2034
telencephalon5.79e-2034
regional part of nervous system7.33e-2094
nervous system7.33e-2094
neural plate1.66e-1986
presumptive neural plate1.66e-1986
regional part of telencephalon2.90e-1933
cerebral hemisphere4.14e-1932
neurectoderm4.84e-1890
regional part of cerebral cortex4.61e-1522
cerebral cortex1.58e-1425
pallium1.58e-1425
ectoderm-derived structure3.18e-14169
neocortex1.33e-1320
ectoderm1.65e-13173
presumptive ectoderm1.65e-13173
pre-chordal neural plate3.46e-1361
head3.48e-13123
anterior region of body2.20e-12129
craniocervical region2.20e-12129
adult organism1.70e-11115
basal ganglion2.59e-079
nuclear complex of neuraxis2.59e-079
aggregate regional part of brain2.59e-079
collection of basal ganglia2.59e-079
cerebral subcortex2.59e-079
nucleus of brain3.65e-079
neural nucleus3.65e-079


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.