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Coexpression cluster:C1782: Difference between revisions

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}}
}}

Revision as of 15:06, 26 November 2012


Full id: C1782_medulloblastoma_putamen_caudate_brain_nucleus_occipital_medial



Phase1 CAGE Peaks

Hg19::chr17:45056606..45056625,-p1@RPRML
Hg19::chr17:45056637..45056648,-p2@RPRML
Hg19::chr3:164913859..164913883,-p5@SLITRK3
Hg19::chr3:164913920..164913931,-p11@SLITRK3
Hg19::chr4:186877864..186877875,-p45@SORBS2


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 nervous system1.33e-8153
regional part of brain1.33e-8153
telencephalon1.25e-7734
cerebral hemisphere1.77e-7732
brain grey matter4.87e-7734
gray matter4.87e-7734
neural tube9.21e-7756
neural rod9.21e-7756
future spinal cord9.21e-7756
neural keel9.21e-7756
brain9.60e-7668
future brain9.60e-7668
regional part of forebrain2.06e-7241
forebrain2.06e-7241
anterior neural tube2.06e-7241
future forebrain2.06e-7241
central nervous system4.70e-7281
regional part of telencephalon7.67e-7232
nervous system5.37e-7089
regional part of cerebral cortex2.94e-6422
neocortex2.28e-5820
cerebral cortex4.00e-5625
pallium4.00e-5625
neurectoderm8.63e-5586
neural plate3.19e-5282
presumptive neural plate3.19e-5282
pre-chordal neural plate3.22e-4961
adult organism4.81e-48114
ecto-epithelium4.33e-39104
ectoderm-derived structure2.54e-36171
ectoderm2.54e-36171
presumptive ectoderm2.54e-36171
structure with developmental contribution from neural crest5.65e-34132
organ system subdivision6.32e-32223
basal ganglion1.66e-229
nuclear complex of neuraxis1.66e-229
aggregate regional part of brain1.66e-229
collection of basal ganglia1.66e-229
cerebral subcortex1.66e-229
neural nucleus8.44e-229
nucleus of brain8.44e-229
gyrus1.81e-196
tube1.07e-17192
telencephalic nucleus8.06e-177
anatomical cluster1.09e-16373
parietal lobe1.26e-165
temporal lobe1.39e-166
occipital lobe1.74e-165
limbic system1.79e-165
corpus striatum2.61e-144
striatum2.61e-144
ventral part of telencephalon2.61e-144
future corpus striatum2.61e-144
anatomical conduit5.18e-13240
brainstem5.75e-126
organ part1.31e-11218
multi-tissue structure2.60e-11342
segmental subdivision of hindbrain3.75e-1112
hindbrain3.75e-1112
presumptive hindbrain3.75e-1112
caudate-putamen4.59e-113
dorsal striatum4.59e-113
frontal cortex1.31e-103
segmental subdivision of nervous system3.20e-1013
small intestine5.89e-104
pons2.44e-093
posterior neural tube9.88e-0915
chordal neural plate9.88e-0915
epithelium9.93e-09306
cell layer1.50e-08309
embryonic structure2.32e-08564
regional part of metencephalon4.55e-089
metencephalon4.55e-089
future metencephalon4.55e-089
embryo6.08e-08592
germ layer6.90e-08560
germ layer / neural crest6.90e-08560
embryonic tissue6.90e-08560
presumptive structure6.90e-08560
germ layer / neural crest derived structure6.90e-08560
epiblast (generic)6.90e-08560
caudate nucleus8.68e-082
future caudate nucleus8.68e-082
developing anatomical structure1.02e-07581
middle temporal gyrus1.37e-072
amygdala1.84e-072
Ammon's horn1.90e-072
lobe parts of cerebral cortex1.90e-072
hippocampal formation1.90e-072
limbic lobe1.90e-072
middle frontal gyrus2.23e-072
globus pallidus3.70e-072
pallidum3.70e-072
organ3.80e-07503
meninx4.89e-072
membrane organ4.89e-072
meningeal cluster4.89e-072


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.

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