Personal tools

Coexpression cluster:C2222

From FANTOM5_SSTAR

Revision as of 14:55, 12 September 2012 by Autoedit (talk | contribs)
Jump to: navigation, search


Full id: C2222_caudate_globus_thalamus_medial_amygdala_putamen_parietal



Phase1 CAGE Peaks

Hg19::chr12:57674546..57674557,-p25@R3HDM2
Hg19::chr1:33360074..33360107,+p1@BC127891
Hg19::chr6:12757225..12757236,+p@chr6:12757225..12757236
+
Hg19::chr6:12955443..12955446,+p@chr6:12955443..12955446
+


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
regional part of forebrain1.18e-3641
forebrain1.18e-3641
future forebrain1.18e-3641
anterior neural tube1.56e-3542
neural tube2.22e-3257
neural rod2.22e-3257
future spinal cord2.22e-3257
neural keel2.22e-3257
cerebral hemisphere1.39e-3132
telencephalon2.80e-3134
regional part of telencephalon6.77e-3033
gray matter2.37e-2934
brain grey matter2.37e-2934
regional part of brain6.11e-2959
regional part of nervous system7.92e-2994
nervous system7.92e-2994
central nervous system3.88e-2882
brain5.47e-2769
future brain5.47e-2769
pre-chordal neural plate1.23e-2561
neural plate2.96e-2286
presumptive neural plate2.96e-2286
neurectoderm7.52e-2290
regional part of cerebral cortex8.11e-2222
cerebral cortex8.01e-2125
pallium8.01e-2125
head6.08e-20123
anterior region of body3.39e-19129
craniocervical region3.39e-19129
neocortex7.97e-1920
ectoderm-derived structure2.19e-17169
ectoderm2.21e-17173
presumptive ectoderm2.21e-17173
adult organism1.46e-13115
basal ganglion3.81e-139
nuclear complex of neuraxis3.81e-139
aggregate regional part of brain3.81e-139
collection of basal ganglia3.81e-139
cerebral subcortex3.81e-139
nucleus of brain5.28e-109
neural nucleus5.28e-109
telencephalic nucleus6.42e-107
limbic system8.57e-105
tube5.32e-09194
corpus striatum2.22e-084
striatum2.22e-084
ventral part of telencephalon2.22e-084
future corpus striatum2.22e-084
anatomical conduit2.57e-08241
temporal lobe3.36e-087
gyrus6.90e-086
anatomical cluster3.04e-07286
organism subdivision5.94e-07365
diencephalon9.85e-077
future diencephalon9.85e-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.