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{{Coexpression_clusters
{{Coexpression_clusters
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|full_id=C4815_merkel_large_carcinoid_medulloblastoma_small_osteosarcoma_Neurons
|full_id=C4815_merkel_large_carcinoid_medulloblastoma_small_osteosarcoma_Neurons
|id=C4815
|id=C4815

Revision as of 17:57, 12 September 2012


Full id: C4815_merkel_large_carcinoid_medulloblastoma_small_osteosarcoma_Neurons



Phase1 CAGE Peaks

Hg19::chr9:23688985..23688989,-p@chr9:23688985..23688989
-
Hg19::chr9:23821808..23821827,-p2@ELAVL2
Hg19::chr9:23821842..23821848,-p8@ELAVL2


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>disease_data<br>

Cell Type
Ontology termp-valuen
ectodermal cell1.34e-1071
neural cell2.59e-1025
neuronal stem cell5.88e-088
epithelial cell3.08e-07254
neurectodermal cell3.85e-0759
neuron9.35e-076
neuroblast9.35e-076
electrically signaling cell9.35e-076
Uber Anatomy
Ontology termp-valuen
ectoderm-derived structure3.41e-40169
ectoderm4.65e-40173
presumptive ectoderm4.65e-40173
regional part of nervous system7.37e-3794
nervous system7.37e-3794
central nervous system3.52e-3682
neural tube2.04e-2957
neural rod2.04e-2957
future spinal cord2.04e-2957
neural keel2.04e-2957
head1.41e-28123
neural plate5.07e-2886
presumptive neural plate5.07e-2886
brain7.86e-2869
future brain7.86e-2869
neurectoderm1.45e-2790
anterior region of body4.22e-27129
craniocervical region4.22e-27129
regional part of brain4.93e-2459
regional part of forebrain3.28e-2241
forebrain3.28e-2241
future forebrain3.28e-2241
gray matter6.36e-2234
brain grey matter6.36e-2234
telencephalon2.02e-2134
anterior neural tube2.65e-2142
cerebral hemisphere2.89e-2132
pre-chordal neural plate8.99e-2161
regional part of telencephalon1.24e-2033
organ part6.30e-18219
cerebral cortex2.41e-1725
pallium2.41e-1725
regional part of cerebral cortex3.04e-1722
neocortex5.76e-1620
adult organism8.98e-14115
organism subdivision1.01e-13365
epithelium3.88e-13309
cell layer1.27e-12312
embryo3.92e-11612
multi-cellular organism1.92e-10659
anatomical conduit2.17e-09241
posterior neural tube3.12e-0915
chordal neural plate3.12e-0915
embryonic structure6.83e-09605
developing anatomical structure6.83e-09605
anatomical system9.24e-09625
anatomical group1.20e-08626
germ layer1.28e-08604
embryonic tissue1.28e-08604
presumptive structure1.28e-08604
epiblast (generic)1.28e-08604
segmental subdivision of nervous system1.75e-0813
segmental subdivision of hindbrain3.84e-0812
hindbrain3.84e-0812
presumptive hindbrain3.84e-0812
multi-tissue structure1.30e-07347
tube3.59e-07194
anatomical cluster9.38e-07286
Disease
Ontology termp-valuen
squamous cell carcinoma4.12e-0714


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#23512233.41052060737530.00117826764536030.00800371347081521



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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