Personal tools

Coexpression cluster:C3089

From FANTOM5_SSTAR

Revision as of 15:55, 26 November 2012 by Autoedit (talk | contribs)
Jump to: navigation, search


Full id: C3089_caudate_pons_diencephalon_locus_parietal_globus_paracentral



Phase1 CAGE Peaks

Hg19::chr11:118023585..118023592,-p7@SCN4B
Hg19::chr11:118023594..118023635,-p2@SCN4B
Hg19::chr11:118023653..118023665,-p5@SCN4B


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
neural tube1.13e-4856
neural rod1.13e-4856
future spinal cord1.13e-4856
neural keel1.13e-4856
adult organism1.21e-48114
regional part of nervous system7.32e-4453
regional part of brain7.32e-4453
central nervous system2.32e-4381
neural plate7.83e-3882
presumptive neural plate7.83e-3882
nervous system1.48e-3789
neurectoderm4.15e-3786
brain8.17e-3768
future brain8.17e-3768
ecto-epithelium2.61e-36104
brain grey matter1.61e-3334
gray matter1.61e-3334
cerebral hemisphere3.82e-3332
telencephalon4.95e-3334
regional part of forebrain5.85e-3341
forebrain5.85e-3341
anterior neural tube5.85e-3341
future forebrain5.85e-3341
regional part of telencephalon3.22e-3032
ectoderm-derived structure6.32e-30171
ectoderm6.32e-30171
presumptive ectoderm6.32e-30171
structure with developmental contribution from neural crest1.00e-24132
organ system subdivision2.47e-24223
pre-chordal neural plate5.13e-2461
cerebral cortex5.21e-2225
pallium5.21e-2225
regional part of cerebral cortex1.91e-2022
neocortex2.05e-2020
posterior neural tube1.30e-1615
chordal neural plate1.30e-1615
anatomical cluster4.08e-16373
neural nucleus2.70e-139
nucleus of brain2.70e-139
multi-tissue structure6.76e-13342
tube1.63e-12192
anatomical conduit1.86e-12240
gyrus6.07e-126
segmental subdivision of hindbrain6.64e-1212
hindbrain6.64e-1212
presumptive hindbrain6.64e-1212
cell layer1.04e-11309
organ part1.12e-11218
epithelium2.27e-11306
segmental subdivision of nervous system8.02e-1113
embryo6.72e-10592
regional part of metencephalon6.91e-109
metencephalon6.91e-109
future metencephalon6.91e-109
telencephalic nucleus7.07e-107
basal ganglion1.03e-099
nuclear complex of neuraxis1.03e-099
aggregate regional part of brain1.03e-099
collection of basal ganglia1.03e-099
cerebral subcortex1.03e-099
organ2.26e-09503
developing anatomical structure5.70e-09581
germ layer1.01e-08560
germ layer / neural crest1.01e-08560
embryonic tissue1.01e-08560
presumptive structure1.01e-08560
germ layer / neural crest derived structure1.01e-08560
epiblast (generic)1.01e-08560
brainstem1.01e-086
corpus striatum1.47e-084
striatum1.47e-084
ventral part of telencephalon1.47e-084
future corpus striatum1.47e-084
embryonic structure1.73e-08564
parietal lobe4.10e-075
pons4.46e-073
occipital lobe5.15e-075
multi-cellular organism6.69e-07656
caudate-putamen8.92e-073
dorsal striatum8.92e-073


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
CTBP2#1488362.71700033932814.049570681927e-060.00012902169385289
ZNF263#1012738.221841637010680.001799043925565870.010894088742516



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.