Personal tools

Coexpression cluster:C3088

From FANTOM5_SSTAR

Revision as of 14:32, 21 May 2012 by Autoedit (talk | contribs)
Jump to: navigation, search


Full id: C3088_duodenum_medial_temporal_olfactory_amygdala_occipital_spinal



Phase1 CAGE Peaks

Hg19::chr11:117712544..117712563,-p@chr11:117712544..117712563
-
Hg19::chr2:149806933..149806951,+p@chr2:149806933..149806951
+
Hg19::chr2:55254388..55254405,-p@chr2:55254388..55254405
-


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>cell_data<br>uberon_data<br><br>


Uber Anatomy
Ontology termp-valuen
adult organism3.01e-36115
neural tube6.11e-3657
neural rod6.11e-3657
future spinal cord6.11e-3657
neural keel6.11e-3657
regional part of nervous system2.73e-3494
nervous system2.73e-3494
central nervous system2.86e-3482
regional part of brain9.98e-2959
regional part of forebrain8.98e-2841
forebrain8.98e-2841
future forebrain8.98e-2841
neurectoderm6.00e-2790
anterior neural tube1.28e-2642
brain2.56e-2669
future brain2.56e-2669
neural plate5.68e-2686
presumptive neural plate5.68e-2686
gray matter5.02e-2534
brain grey matter5.02e-2534
telencephalon7.34e-2534
regional part of telencephalon4.08e-2433
cerebral hemisphere1.67e-2332
cerebral cortex3.68e-1925
pallium3.68e-1925
pre-chordal neural plate6.27e-1961
ectoderm1.45e-17173
presumptive ectoderm1.45e-17173
regional part of cerebral cortex2.58e-1722
ectoderm-derived structure1.16e-16169
neocortex7.95e-1620
anterior region of body2.57e-13129
craniocervical region2.57e-13129
head5.21e-13123
embryo1.78e-12612
organ1.72e-10511
posterior neural tube2.63e-1015
chordal neural plate2.63e-1015
embryonic structure3.30e-10605
developing anatomical structure3.30e-10605
germ layer7.47e-10604
embryonic tissue7.47e-10604
presumptive structure7.47e-10604
epiblast (generic)7.47e-10604
multi-cellular organism1.70e-09659
segmental subdivision of nervous system4.19e-0913
segmental subdivision of hindbrain2.29e-0812
hindbrain2.29e-0812
presumptive hindbrain2.29e-0812
anatomical system4.48e-08625
anatomical group5.99e-08626
basal ganglion1.90e-079
nuclear complex of neuraxis1.90e-079
aggregate regional part of brain1.90e-079
collection of basal ganglia1.90e-079
cerebral subcortex1.90e-079
nucleus of brain2.66e-079
neural nucleus2.66e-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.