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Coexpression cluster:C3981

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Full id: C3981_Astrocyte_trachea_Chondrocyte_Ciliary_retina_Retinal_merkel



Phase1 CAGE Peaks

Hg19::chr1:40782923..40782936,-p4@COL9A2
Hg19::chr1:40782938..40782974,-p1@COL9A2
Hg19::chr1:40782976..40782993,-p5@COL9A2


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><br>uberon_data<br><br>


Uber Anatomy
Ontology termp-valuen
neural plate4.57e-3686
presumptive neural plate4.57e-3686
neurectoderm1.19e-3490
regional part of nervous system3.56e-3394
nervous system3.56e-3394
neural tube9.86e-3357
neural rod9.86e-3357
future spinal cord9.86e-3357
neural keel9.86e-3357
central nervous system1.99e-3182
regional part of brain3.50e-3059
pre-chordal neural plate1.05e-2861
adult organism1.93e-26115
ectoderm-derived structure1.01e-25169
ectoderm2.92e-25173
presumptive ectoderm2.92e-25173
brain2.97e-2469
future brain2.97e-2469
anterior region of body3.91e-24129
craniocervical region3.91e-24129
anterior neural tube4.35e-2442
regional part of forebrain7.23e-2441
forebrain7.23e-2441
future forebrain7.23e-2441
head1.58e-23123
telencephalon2.91e-2234
gray matter3.98e-2234
brain grey matter3.98e-2234
regional part of telencephalon1.47e-2133
cerebral hemisphere1.24e-2032
cerebral cortex2.53e-1625
pallium2.53e-1625
organism subdivision1.28e-14365
organ part1.66e-14219
regional part of cerebral cortex6.13e-1422
epithelium1.58e-13309
cell layer2.74e-13312
neocortex6.04e-1320
multi-tissue structure4.21e-12347
anatomical cluster1.36e-11286
tube2.35e-11194
anatomical conduit4.17e-10241
posterior neural tube1.09e-0915
chordal neural plate1.09e-0915
segmental subdivision of nervous system1.43e-0813
pigment epithelium of eye7.96e-0811
segmental subdivision of hindbrain8.26e-0812
hindbrain8.26e-0812
presumptive hindbrain8.26e-0812
sensory system1.04e-0724
entire sense organ system1.04e-0724
visual system1.18e-0721
cavitated compound organ2.14e-0732
nucleus of brain2.89e-079
neural nucleus2.89e-079
sense organ4.55e-0723
mesonephros5.09e-0718
pronephros5.09e-0718
nephrogenic cord5.09e-0718
pronephric mesoderm5.09e-0718
rostral part of nephrogenic cord5.09e-0718
presumptive pronephric mesoderm5.09e-0718
eye5.45e-0720
face6.81e-0721
basal ganglion6.98e-079
nuclear complex of neuraxis6.98e-079
aggregate regional part of brain6.98e-079
collection of basal ganglia6.98e-079
cerebral subcortex6.98e-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.