Personal tools

Coexpression cluster:C1075

From FANTOM5_SSTAR

Revision as of 16:50, 8 August 2012 by Autoedit (talk | contribs)
Jump to: navigation, search


Full id: C1075_parietal_hippocampus_medulla_locus_caudate_thalamus_occipital



Phase1 CAGE Peaks

Hg19::chr2:115609753..115609755,+p@chr2:115609753..115609755
+
Hg19::chr4:151171746..151171764,+p@chr4:151171746..151171764
+
Hg19::chr4:151171800..151171822,+p@chr4:151171800..151171822
+
Hg19::chr4:151171843..151171859,+p@chr4:151171843..151171859
+
Hg19::chr4:151171861..151171883,+p@chr4:151171861..151171883
+
Hg19::chr4:151171897..151171959,+p@chr4:151171897..151171959
+
Hg19::chr4:151171963..151171987,+p@chr4:151171963..151171987
+
Hg19::chr8:63161215..63161235,+p5@NKAIN3


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><br>uberon_data<br><br>


Uber Anatomy
Ontology termp-valuen
central nervous system5.76e-3982
regional part of nervous system3.56e-3794
nervous system3.56e-3794
neural tube2.86e-3657
neural rod2.86e-3657
future spinal cord2.86e-3657
neural keel2.86e-3657
brain5.76e-3569
future brain5.76e-3569
regional part of brain2.24e-3059
regional part of forebrain6.62e-3041
forebrain6.62e-3041
future forebrain6.62e-3041
neurectoderm2.27e-2990
neural plate5.51e-2986
presumptive neural plate5.51e-2986
anterior neural tube1.33e-2842
adult organism1.68e-25115
gray matter2.86e-2534
brain grey matter2.86e-2534
telencephalon3.64e-2534
regional part of telencephalon1.61e-2433
cerebral hemisphere9.97e-2432
pre-chordal neural plate1.16e-2161
ectoderm1.29e-20173
presumptive ectoderm1.29e-20173
head3.46e-20123
ectoderm-derived structure5.12e-20169
anterior region of body2.21e-19129
craniocervical region2.21e-19129
cerebral cortex6.84e-1925
pallium6.84e-1925
regional part of cerebral cortex2.53e-1722
neocortex9.53e-1620
posterior neural tube9.01e-0915
chordal neural plate9.01e-0915
organism subdivision2.80e-08365
basal ganglion6.99e-089
nuclear complex of neuraxis6.99e-089
aggregate regional part of brain6.99e-089
collection of basal ganglia6.99e-089
cerebral subcortex6.99e-089
nucleus of brain8.21e-089
neural nucleus8.21e-089
organ4.63e-07511
temporal lobe9.06e-077


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.