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Coexpression cluster:C2913

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Full id: C2913_extraskeletal_nonsmall_chronic_parietal_occipital_putamen_duodenum



Phase1 CAGE Peaks

Hg19::chr8:114449458..114449469,-p8@CSMD3
Hg19::chr8:114449484..114449517,-p2@CSMD3
Hg19::chr8:114449556..114449571,-p5@CSMD3
Hg19::chr8:114449595..114449607,-p6@CSMD3


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 tube1.01e-7056
neural rod1.01e-7056
future spinal cord1.01e-7056
neural keel1.01e-7056
regional part of nervous system3.03e-6753
regional part of brain3.03e-6753
central nervous system1.39e-6181
regional part of forebrain1.73e-5841
forebrain1.73e-5841
anterior neural tube1.73e-5841
future forebrain1.73e-5841
brain2.12e-5868
future brain2.12e-5868
nervous system2.34e-5489
telencephalon1.14e-5334
brain grey matter1.19e-5334
gray matter1.19e-5334
cerebral hemisphere3.19e-4932
regional part of telencephalon5.34e-4932
neurectoderm1.68e-4786
neural plate4.28e-4582
presumptive neural plate4.28e-4582
regional part of cerebral cortex2.06e-4122
pre-chordal neural plate9.49e-3761
neocortex2.72e-3620
cerebral cortex5.20e-3625
pallium5.20e-3625
ecto-epithelium2.21e-35104
adult organism7.20e-31114
structure with developmental contribution from neural crest3.15e-30132
ectoderm-derived structure3.49e-27171
ectoderm3.49e-27171
presumptive ectoderm3.49e-27171
organ system subdivision4.25e-20223
basal ganglion4.69e-209
nuclear complex of neuraxis4.69e-209
aggregate regional part of brain4.69e-209
collection of basal ganglia4.69e-209
cerebral subcortex4.69e-209
neural nucleus3.53e-199
nucleus of brain3.53e-199
limbic system2.23e-155
tube2.37e-15192
temporal lobe6.13e-156
telencephalic nucleus1.61e-147
posterior neural tube2.06e-1315
chordal neural plate2.06e-1315
corpus striatum1.02e-124
striatum1.02e-124
ventral part of telencephalon1.02e-124
future corpus striatum1.02e-124
gyrus1.10e-116
brainstem3.13e-116
organ part1.92e-10218
segmental subdivision of hindbrain2.61e-1012
hindbrain2.61e-1012
presumptive hindbrain2.61e-1012
anatomical conduit3.12e-10240
caudate-putamen5.46e-103
dorsal striatum5.46e-103
occipital lobe1.31e-095
parietal lobe1.53e-095
segmental subdivision of nervous system1.95e-0913
pons4.99e-093
anatomical cluster8.06e-08373
regional part of metencephalon1.42e-079
metencephalon1.42e-079
future metencephalon1.42e-079
amygdala2.12e-072
caudate nucleus4.22e-072
future caudate nucleus4.22e-072
Ammon's horn6.37e-072
lobe parts of cerebral cortex6.37e-072
hippocampal formation6.37e-072
limbic lobe6.37e-072
diencephalon9.61e-077
future diencephalon9.61e-077


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.