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Coexpression cluster:C2686

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Full id: C2686_Neural_Ciliary_Astrocyte_neuroblastoma_Lens_teratocarcinoma_Neurons



Phase1 CAGE Peaks

Hg19::chr2:210798655..210798664,+p@chr2:210798655..210798664
+
Hg19::chr3:147657737..147657747,+p2@ENST00000467198
Hg19::chr9:117880804..117880815,-p4@TNC
Hg19::chr9:117880865..117880885,-p3@TNC


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


GO IDGO nameFDR corrected p-value
GO:0007528neuromuscular junction development0.00824208171435299
GO:0050808synapse organization and biogenesis0.00865418580007064
GO:0048741skeletal muscle fiber development0.00865418580007064
GO:0048747muscle fiber development0.00865418580007064
GO:0007519skeletal muscle development0.0090662898857883
GO:0005604basement membrane0.0090662898857883
GO:0043062extracellular structure organization and biogenesis0.0090662898857883
GO:0014706striated muscle development0.0090662898857883
GO:0044420extracellular matrix part0.0119968078286694
GO:0007517muscle development0.0141763805486871
GO:0005578proteinaceous extracellular matrix0.0315446945612964



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
neural cell7.08e-0925
non-terminally differentiated cell4.91e-08180
oligodendrocyte1.45e-077
macroglial cell1.45e-077
astrocyte1.45e-077
oligodendrocyte precursor cell1.45e-077
neurectodermal cell6.37e-0759
Uber Anatomy
Ontology termp-valuen
central nervous system5.95e-1682
regional part of nervous system1.24e-1494
nervous system1.24e-1494
ectoderm1.16e-12173
presumptive ectoderm1.16e-12173
ectoderm-derived structure6.94e-12169
neurectoderm3.36e-1090
neural tube5.55e-1057
neural rod5.55e-1057
future spinal cord5.55e-1057
neural keel5.55e-1057
brain7.66e-1069
future brain7.66e-1069
neural plate2.09e-0986
presumptive neural plate2.09e-0986
regional part of brain3.77e-0959
head1.10e-08123
anterior region of body1.72e-08129
craniocervical region1.72e-08129
organism subdivision7.52e-08365


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
CTBP2#1488231.35850016966410.001492676882047230.00954178485029567
ESR1#2099215.38430164807720.006065572629693510.0268413346838083
NANOG#79923214.62238924050630.006698757715363760.0284927733581036



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.