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Coexpression cluster:C3890


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Full id: C3890_spinal_amygdala_locus_medulla_hippocampus_optic_globus

Phase1 CAGE Peaks


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
neural tube8.48e-2957
neural rod8.48e-2957
future spinal cord8.48e-2957
neural keel8.48e-2957
central nervous system5.73e-2782
regional part of brain1.73e-2659
neural plate8.17e-2686
presumptive neural plate8.17e-2686
future brain8.50e-2569
regional part of nervous system4.26e-2394
nervous system4.26e-2394
cell layer1.24e-22312
anatomical conduit1.70e-21241
anatomical group2.07e-21626
anatomical system2.89e-21625
organism subdivision8.66e-21365
ectoderm-derived structure1.31e-20169
multi-cellular organism3.54e-20659
anterior neural tube5.08e-2042
regional part of forebrain5.66e-2041
future forebrain5.66e-2041
gray matter3.00e-1934
brain grey matter3.00e-1934
presumptive ectoderm9.93e-19173
anatomical cluster1.47e-18286
regional part of telencephalon1.55e-1833
cerebral hemisphere8.06e-1832
anterior region of body9.14e-18129
craniocervical region9.14e-18129
pre-chordal neural plate1.68e-1761
embryonic structure1.57e-14605
developing anatomical structure1.57e-14605
germ layer1.71e-14604
embryonic tissue1.71e-14604
presumptive structure1.71e-14604
epiblast (generic)1.71e-14604
cerebral cortex1.52e-1325
splanchnic layer of lateral plate mesoderm2.35e-1284
regional part of cerebral cortex3.29e-1222
vascular system2.28e-1179
organ part1.11e-10219
blood vessel1.11e-1060
epithelial tube open at both ends1.11e-1060
blood vasculature1.11e-1060
vascular cord1.11e-1060
arterial blood vessel2.26e-1042
arterial system2.26e-1042
posterior neural tube5.53e-1015
chordal neural plate5.53e-1015
segmental subdivision of nervous system1.10e-0813
multi-tissue structure2.29e-08347
paraxial mesoderm4.05e-0883
presomitic mesoderm4.05e-0883
presumptive segmental plate4.05e-0883
trunk paraxial mesoderm4.05e-0883
presumptive paraxial mesoderm4.05e-0883
adult organism4.44e-08115
segmental subdivision of hindbrain4.80e-0812
presumptive hindbrain4.80e-0812
systemic artery4.94e-0833
systemic arterial system4.94e-0833
epithelial tube2.27e-07118
multilaminar epithelium2.64e-0782
basal ganglion2.82e-079
nuclear complex of neuraxis2.82e-079
aggregate regional part of brain2.82e-079
collection of basal ganglia2.82e-079
cerebral subcortex2.82e-079
nucleus of brain2.88e-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



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.