Personal tools

Coexpression cluster:C1316

From FANTOM5_SSTAR

Revision as of 13:50, 12 September 2012 by Autoedit (talk | contribs)
Jump to: navigation, search


Full id: C1316_cerebellum_thalamus_globus_substantia_occipital_hippocampus_middle



Phase1 CAGE Peaks

Hg19::chr10:594847..594852,-p@chr10:594847..594852
-
Hg19::chr10:94000428..94000487,-p4@CPEB3
Hg19::chr19:21603457..21603460,+p@chr19:21603457..21603460
+
Hg19::chr1:65533390..65533443,-p1@ENST00000448344
Hg19::chr2:70313393..70313424,-p1@PCBP1-AS1
Hg19::chr9:14314946..14314983,-p8@NFIB


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
adult organism1.47e-52115
neural tube6.69e-3157
neural rod6.69e-3157
future spinal cord6.69e-3157
neural keel6.69e-3157
anterior neural tube1.22e-2542
central nervous system1.52e-2582
regional part of brain2.91e-2559
regional part of forebrain3.22e-2541
forebrain3.22e-2541
future forebrain3.22e-2541
regional part of nervous system2.93e-2494
nervous system2.93e-2494
brain8.71e-2369
future brain8.71e-2369
gray matter3.85e-2134
brain grey matter3.85e-2134
telencephalon5.03e-2134
regional part of telencephalon1.92e-2033
cerebral hemisphere1.03e-1932
neurectoderm5.24e-1990
neural plate2.97e-1886
presumptive neural plate2.97e-1886
cerebral cortex2.43e-1525
pallium2.43e-1525
regional part of cerebral cortex5.13e-1522
pre-chordal neural plate7.95e-1461
neocortex1.01e-1320
anterior region of body2.97e-09129
craniocervical region2.97e-09129
ectoderm1.21e-08173
presumptive ectoderm1.21e-08173
head2.49e-08123
ectoderm-derived structure4.50e-08169
nucleus of brain2.73e-079
neural nucleus2.73e-079
basal ganglion3.52e-079
nuclear complex of neuraxis3.52e-079
aggregate regional part of brain3.52e-079
collection of basal ganglia3.52e-079
cerebral subcortex3.52e-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


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

TF#promotersEnrichmentp-valueq-value
MAX#414944.301703672671410.006644923910676370.0282926009338795



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.