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Coexpression cluster:C2939

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Full id: C2939_neuroblastoma_middle_occipital_parietal_medial_olfactory_smallcell



Phase1 CAGE Peaks

Hg19::chr9:136465122..136465132,-p2@AK124587
Hg19::chr9:136465213..136465223,-p@chr9:136465213..136465223
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Hg19::chr9:136465441..136465483,-p@chr9:136465441..136465483
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Hg19::chr9:136465528..136465544,-p@chr9:136465528..136465544
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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 tube3.55e-7756
neural rod3.55e-7756
future spinal cord3.55e-7756
neural keel3.55e-7756
regional part of nervous system2.39e-7353
regional part of brain2.39e-7353
telencephalon5.00e-6634
brain grey matter1.13e-6534
gray matter1.13e-6534
cerebral hemisphere2.17e-6532
brain8.90e-6568
future brain8.90e-6568
regional part of cerebral cortex4.57e-6322
regional part of forebrain2.42e-6241
forebrain2.42e-6241
anterior neural tube2.42e-6241
future forebrain2.42e-6241
regional part of telencephalon3.60e-6032
central nervous system4.37e-5981
nervous system2.13e-5889
neocortex6.97e-5720
neurectoderm3.71e-5686
cerebral cortex4.08e-5525
pallium4.08e-5525
neural plate7.12e-5382
presumptive neural plate7.12e-5382
pre-chordal neural plate1.12e-4261
ecto-epithelium4.19e-42104
adult organism2.43e-31114
structure with developmental contribution from neural crest3.20e-31132
ectoderm-derived structure7.99e-31171
ectoderm7.99e-31171
presumptive ectoderm7.99e-31171
organ system subdivision1.43e-23223
gyrus6.84e-216
tube1.20e-19192
occipital lobe9.89e-185
parietal lobe1.30e-175
posterior neural tube1.25e-1515
chordal neural plate1.25e-1515
anatomical conduit9.26e-14240
temporal lobe6.08e-136
brainstem1.28e-126
neural nucleus2.18e-129
nucleus of brain2.18e-129
segmental subdivision of hindbrain3.50e-1212
hindbrain3.50e-1212
presumptive hindbrain3.50e-1212
limbic system2.00e-115
frontal cortex2.26e-113
organ part2.62e-11218
segmental subdivision of nervous system3.60e-1113
epithelium3.42e-10306
cell layer5.35e-10309
pons8.14e-103
anatomical cluster9.32e-10373
basal ganglion3.53e-099
nuclear complex of neuraxis3.53e-099
aggregate regional part of brain3.53e-099
collection of basal ganglia3.53e-099
cerebral subcortex3.53e-099
regional part of metencephalon7.00e-099
metencephalon7.00e-099
future metencephalon7.00e-099
middle temporal gyrus2.69e-082
middle frontal gyrus4.24e-082
corpus striatum4.77e-084
striatum4.77e-084
ventral part of telencephalon4.77e-084
future corpus striatum4.77e-084
Ammon's horn9.03e-082
lobe parts of cerebral cortex9.03e-082
hippocampal formation9.03e-082
limbic lobe9.03e-082
telencephalic nucleus1.11e-077
dorsal plus ventral thalamus1.65e-072
thalamic complex1.65e-072
multi-tissue structure1.81e-07342
locus ceruleus3.41e-072
brainstem nucleus3.41e-072
hindbrain nucleus3.41e-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


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

TF#promotersEnrichmentp-valueq-value
SUZ12#23512225.05789045553150.002325256716520610.0131881984477406



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.