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Coexpression cluster:C1991

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Full id: C1991_small_extraskeletal_non_acute_lymphoma_neuroblastoma_pineal



Phase1 CAGE Peaks

Hg19::chr7:18535346..18535399,+p1@HDAC9
Hg19::chr7:18535786..18535808,+p12@HDAC9
Hg19::chr7:18535844..18535853,+p35@HDAC9
Hg19::chr7:18535854..18535890,+p8@HDAC9
Hg19::chr7:18535893..18535918,+p10@HDAC9


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><br>


Cell Type
Ontology termp-valuen
lymphocyte of B lineage2.61e-0824
pro-B cell2.61e-0824
B cell6.66e-0814
neural cell1.89e-0725
Uber Anatomy
Ontology termp-valuen
adult organism4.06e-33115
regional part of nervous system3.35e-3194
nervous system3.35e-3194
central nervous system5.07e-2982
neural tube8.15e-2857
neural rod8.15e-2857
future spinal cord8.15e-2857
neural keel8.15e-2857
regional part of forebrain3.02e-2441
forebrain3.02e-2441
future forebrain3.02e-2441
brain5.05e-2369
future brain5.05e-2369
anterior neural tube5.42e-2342
regional part of brain1.60e-2259
neural plate1.50e-2086
presumptive neural plate1.50e-2086
telencephalon2.55e-2034
gray matter4.75e-2034
brain grey matter4.75e-2034
neurectoderm9.84e-2090
regional part of telencephalon1.08e-1933
cerebral hemisphere1.81e-1932
cerebral cortex1.01e-1625
pallium1.01e-1625
pre-chordal neural plate1.98e-1561
regional part of cerebral cortex8.64e-1522
ectoderm-derived structure3.72e-14169
ectoderm6.87e-14173
presumptive ectoderm6.87e-14173
neocortex9.72e-1420
anterior region of body1.76e-12129
craniocervical region1.76e-12129
head2.97e-12123


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
EP300#203356.77394172622327.00901578206049e-050.00111012223121416
ZNF263#1012746.577473309608540.0009875103237900160.00709560307576921



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.