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Coexpression cluster:C3054

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Full id: C3054_mature_locus_thalamus_pons_amygdala_diencephalon_hippocampus



Phase1 CAGE Peaks

Hg19::chr10:88718314..88718388,+p1@SNCG
Hg19::chr1:161101568..161101584,+p@chr1:161101568..161101584
+
Hg19::chr1:27120942..27120945,-p@chr1:27120942..27120945
-


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>


Uber Anatomy
Ontology termp-valuen
anatomical cluster5.80e-37286
anatomical conduit4.66e-34241
adult organism4.88e-33115
epithelium1.19e-27309
cell layer1.85e-27312
tube2.01e-27194
neural tube5.99e-2457
neural rod5.99e-2457
future spinal cord5.99e-2457
neural keel5.99e-2457
multi-tissue structure1.68e-23347
neural plate4.02e-2286
presumptive neural plate4.02e-2286
organ part9.08e-21219
multi-cellular organism1.76e-20659
regional part of brain3.23e-2059
neurectoderm4.61e-2090
organism subdivision1.38e-19365
anatomical system1.67e-19625
anatomical group3.54e-19626
head8.24e-19123
anterior region of body4.86e-18129
craniocervical region4.86e-18129
brain1.88e-1769
future brain1.88e-1769
anterior neural tube4.37e-1742
regional part of forebrain1.61e-1641
forebrain1.61e-1641
future forebrain1.61e-1641
central nervous system1.81e-1682
embryo7.21e-16612
gray matter4.80e-1534
brain grey matter4.80e-1534
pre-chordal neural plate7.78e-1561
embryonic structure9.60e-15605
developing anatomical structure9.60e-15605
telencephalon1.01e-1434
germ layer1.63e-14604
embryonic tissue1.63e-14604
presumptive structure1.63e-14604
epiblast (generic)1.63e-14604
regional part of nervous system3.56e-1494
nervous system3.56e-1494
regional part of telencephalon3.74e-1433
cerebral hemisphere5.75e-1432
ectoderm-derived structure9.51e-14169
ectoderm8.65e-13173
presumptive ectoderm8.65e-13173
regional part of cerebral cortex1.12e-1122
organ5.00e-11511
neocortex1.84e-1020
vessel3.76e-1069
cerebral cortex4.62e-1025
pallium4.62e-1025
vasculature6.23e-1079
vascular system6.23e-1079
compound organ2.32e-0969
organ segment2.80e-0997
splanchnic layer of lateral plate mesoderm3.60e-0984
epithelial tube1.01e-08118
blood vessel3.05e-0860
epithelial tube open at both ends3.05e-0860
blood vasculature3.05e-0860
vascular cord3.05e-0860
posterior neural tube4.19e-0815
chordal neural plate4.19e-0815
endothelium8.38e-0818
blood vessel endothelium8.38e-0818
cardiovascular system endothelium8.38e-0818
simple squamous epithelium1.91e-0722
squamous epithelium2.50e-0725
primordium4.50e-07168
respiratory system7.34e-0772
segmental subdivision of nervous system9.42e-0713


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.