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|ontology_enrichment_disease=
|ontology_enrichment_disease=
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}}
}}

Revision as of 18:19, 8 August 2012


Full id: C2465_small_peripheral_acute_lymphoma_diffuse_Neural_merkel



Phase1 CAGE Peaks

Hg19::chr18:53089453..53089482,-p11@TCF4
Hg19::chr18:53089493..53089517,-p15@TCF4
Hg19::chr18:53089521..53089533,-p22@TCF4
Hg19::chr18:53089538..53089578,-p14@TCF4


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
adult organism1.57e-37115
neural tube9.85e-2657
neural rod9.85e-2657
future spinal cord9.85e-2657
neural keel9.85e-2657
regional part of nervous system1.66e-2494
nervous system1.66e-2494
central nervous system9.41e-2482
ectoderm4.98e-22173
presumptive ectoderm4.98e-22173
ectoderm-derived structure5.07e-21169
brain3.33e-2069
future brain3.33e-2069
regional part of brain6.21e-2059
anterior neural tube1.27e-1942
regional part of forebrain4.81e-1941
forebrain4.81e-1941
future forebrain4.81e-1941
neurectoderm8.48e-1990
neural plate8.06e-1886
presumptive neural plate8.06e-1886
anterior region of body9.23e-18129
craniocervical region9.23e-18129
head1.03e-16123
telencephalon2.13e-1634
gray matter5.36e-1634
brain grey matter5.36e-1634
regional part of telencephalon7.42e-1633
cerebral hemisphere2.90e-1532
organism subdivision3.64e-13365
cerebral cortex2.50e-1225
pallium2.50e-1225
regional part of cerebral cortex2.62e-1222
neocortex1.06e-1120
anatomical conduit1.94e-11241
pre-chordal neural plate2.12e-1161
multi-cellular organism2.23e-10659
anatomical system2.72e-09625
anatomical group3.86e-09626
anatomical cluster1.13e-08286
posterior neural tube2.68e-0715
chordal neural plate2.68e-0715
epithelium3.97e-07309
tube4.64e-07194


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.