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|ontology_enrichment_disease=DOID:305!1.39e-09!106;DOID:0050687!5.68e-08!143
|ontology_enrichment_disease=DOID:305!1.39e-09!106;DOID:0050687!5.68e-08!143
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}}

Revision as of 17:12, 8 August 2012


Full id: C1364_Hepatocyte_liver_occipital_cerebellum_somatostatinoma_small_pancreas



Phase1 CAGE Peaks

Hg19::chr12:56881874..56881907,-p4@GLS2
Hg19::chr12:56881909..56881935,-p3@GLS2
Hg19::chr12:56881937..56881963,-p2@GLS2
Hg19::chr12:56881973..56881980,-p6@GLS2
Hg19::chr12:56882118..56882125,-p9@GLS2
Hg19::chr12:56882136..56882197,-p1@GLS2


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>disease_data<br>


Uber Anatomy
Ontology termp-valuen
adult organism9.54e-35115
neural tube8.76e-2957
neural rod8.76e-2957
future spinal cord8.76e-2957
neural keel8.76e-2957
central nervous system3.09e-2782
regional part of nervous system5.84e-2694
nervous system5.84e-2694
regional part of forebrain2.15e-2341
forebrain2.15e-2341
future forebrain2.15e-2341
anterior neural tube3.20e-2342
regional part of brain7.58e-2359
brain9.45e-2369
future brain9.45e-2369
neural plate4.57e-2186
presumptive neural plate4.57e-2186
neurectoderm1.23e-2090
gray matter1.55e-1934
brain grey matter1.55e-1934
telencephalon2.58e-1934
ectoderm-derived structure3.44e-19169
ectoderm3.99e-19173
presumptive ectoderm3.99e-19173
cerebral hemisphere5.89e-1932
regional part of telencephalon1.21e-1833
pre-chordal neural plate1.07e-1661
regional part of cerebral cortex4.75e-1622
anterior region of body1.15e-15129
craniocervical region1.15e-15129
head2.29e-15123
neocortex7.40e-1520
cerebral cortex1.27e-1425
pallium1.27e-1425
anatomical conduit5.04e-08241
organ part8.07e-08219
tube2.60e-07194
posterior neural tube7.70e-0715
chordal neural plate7.70e-0715
Disease
Ontology termp-valuen
carcinoma1.39e-09106
cell type cancer5.68e-08143


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)

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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.