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Coexpression cluster:C2996

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Full id: C2996_optic_CD4_corpus_thalamus_globus_spinal_diencephalon



Phase1 CAGE Peaks

Hg19::chr10:14613932..14613943,-p9@FAM107B
Hg19::chr10:14613968..14614048,-p2@FAM107B
Hg19::chr5:80256453..80256506,+p2@RASGRF2


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:0005089Rho guanyl-nucleotide exchange factor activity0.0470387377840574
GO:0035023regulation of Rho protein signal transduction0.0470387377840574
GO:0005088Ras guanyl-nucleotide exchange factor activity0.0470387377840574
GO:0007266Rho protein signal transduction0.0470387377840574



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
mature alpha-beta T cell2.03e-1118
alpha-beta T cell2.03e-1118
immature T cell2.03e-1118
mature T cell2.03e-1118
immature alpha-beta T cell2.03e-1118
CD8-positive, alpha-beta T cell8.99e-0911
T cell7.04e-0725
pro-T cell7.04e-0725
Uber Anatomy
Ontology termp-valuen
adult organism7.05e-43115
neural plate1.70e-2386
presumptive neural plate1.70e-2386
neural tube9.15e-2357
neural rod9.15e-2357
future spinal cord9.15e-2357
neural keel9.15e-2357
neurectoderm9.85e-2190
regional part of brain3.07e-2059
central nervous system6.14e-2082
brain5.83e-1869
future brain5.83e-1869
regional part of nervous system3.56e-1794
nervous system3.56e-1794
pre-chordal neural plate3.79e-1761
anterior region of body4.17e-17129
craniocervical region4.17e-17129
anterior neural tube7.75e-1742
regional part of forebrain1.03e-1641
forebrain1.03e-1641
future forebrain1.03e-1641
head6.61e-16123
telencephalon1.66e-1534
gray matter2.00e-1534
brain grey matter2.00e-1534
regional part of telencephalon6.77e-1533
cerebral hemisphere3.32e-1432
ectoderm-derived structure3.87e-12169
anatomical conduit6.05e-11241
ectoderm6.21e-11173
presumptive ectoderm6.21e-11173
anatomical cluster7.17e-11286
regional part of cerebral cortex1.41e-1022
cerebral cortex3.40e-1025
pallium3.40e-1025
neocortex1.66e-0920
tube3.80e-09194
organ part2.06e-07219
posterior neural tube3.74e-0715
chordal neural plate3.74e-0715
nucleus of brain5.50e-079
neural nucleus5.50e-079
basal ganglion9.36e-079
nuclear complex of neuraxis9.36e-079
aggregate regional part of brain9.36e-079
collection of basal ganglia9.36e-079
cerebral subcortex9.36e-079


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


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.