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{{Coexpression_clusters
{{Coexpression_clusters
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|full_id=C1024_Pericytes_cerebellum_neuroblastoma_HES3GFP_iPS_extraskeletal_teratocarcinoma
|full_id=C1024_Pericytes_cerebellum_neuroblastoma_HES3GFP_iPS_extraskeletal_teratocarcinoma
|id=C1024
|id=C1024

Revision as of 13:26, 12 September 2012


Full id: C1024_Pericytes_cerebellum_neuroblastoma_HES3GFP_iPS_extraskeletal_teratocarcinoma



Phase1 CAGE Peaks

Hg19::chr13:100623360..100623373,-p2@ZIC5
Hg19::chr13:100623375..100623425,-p1@ZIC5
Hg19::chr13:100633445..100633468,+p1@AK298232
Hg19::chr13:100633480..100633490,+p3@AK298232
Hg19::chr13:100634031..100634045,+p1@ZIC2
Hg19::chr13:100634809..100634826,+p11@ZIC2
Hg19::chr13:100638100..100638115,+p4@ZIC2
Hg19::chr13:100638124..100638136,+p7@ZIC2


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
neural cell2.48e-1025
neurectodermal cell1.76e-0759
neuronal stem cell5.49e-078
Uber Anatomy
Ontology termp-valuen
central nervous system6.94e-4482
regional part of nervous system9.37e-4194
nervous system9.37e-4194
brain8.90e-3569
future brain8.90e-3569
regional part of brain3.67e-3059
neural tube1.66e-2957
neural rod1.66e-2957
future spinal cord1.66e-2957
neural keel1.66e-2957
neurectoderm3.96e-2990
neural plate2.90e-2686
presumptive neural plate2.90e-2686
ectoderm4.33e-24173
presumptive ectoderm4.33e-24173
ectoderm-derived structure8.59e-22169
regional part of forebrain9.16e-2141
forebrain9.16e-2141
future forebrain9.16e-2141
anterior neural tube7.43e-2042
head9.56e-20123
pre-chordal neural plate1.41e-1861
telencephalon1.61e-1834
anterior region of body3.12e-18129
craniocervical region3.12e-18129
regional part of telencephalon6.00e-1833
gray matter6.00e-1834
brain grey matter6.00e-1834
cerebral hemisphere2.13e-1732
cerebral cortex2.65e-1525
pallium2.65e-1525
regional part of cerebral cortex1.76e-1322
neocortex3.22e-1220
posterior neural tube5.96e-1115
chordal neural plate5.96e-1115
segmental subdivision of hindbrain2.09e-0912
hindbrain2.09e-0912
presumptive hindbrain2.09e-0912
segmental subdivision of nervous system2.12e-0913
regional part of metencephalon1.37e-079
metencephalon1.37e-079
future metencephalon1.37e-079
adult organism6.69e-07115
Disease
Ontology termp-valuen
cell type cancer1.04e-29143
cancer1.50e-29235
disease of cellular proliferation9.29e-28239
carcinoma7.08e-21106
germ cell and embryonal cancer3.51e-0822
germ cell cancer3.51e-0822
organ system cancer4.93e-08137
adenocarcinoma4.64e-0725


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
E2F6#187653.135722332310870.01024880501420960.0381472948743376
EGR1#195853.117611934256340.01051390990388360.0389204351345726
ZNF263#1012755.138651023131670.001082531249033560.00763805439250206



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.