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Coexpression cluster:C759

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Full id: C759_nonsmall_gastrointestinal_occipital_pineal_cerebellum_small_argyrophil



Phase1 CAGE Peaks

Hg19::chr15:48483855..48483892,+p1@CTXN2
p2@SLC12A1
Hg19::chr18:40857274..40857292,-p5@SYT4
Hg19::chr18:40857296..40857305,-p8@SYT4
Hg19::chr18:40857329..40857357,-p2@SYT4
Hg19::chr18:40857368..40857384,-p6@SYT4
Hg19::chr18:40857389..40857405,-p3@SYT4
Hg19::chr18:40857447..40857461,-p1@SYT4
Hg19::chr18:40857470..40857481,-p7@SYT4
Hg19::chr18:40857484..40857491,-p9@SYT4
Hg19::chr18:40857493..40857505,-p4@SYT4
Hg19::chr6:158957739..158957759,+p3@TMEM181


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:0007269neurotransmitter secretion0.0360628509212003
GO:0045055regulated secretory pathway0.0360628509212003
GO:0048471perinuclear region of cytoplasm0.0360628509212003
GO:0003001generation of a signal involved in cell-cell signaling0.0360628509212003
GO:0008021synaptic vesicle0.0360628509212003
GO:0001505regulation of neurotransmitter levels0.0360628509212003
GO:0043005neuron projection0.0360628509212003
GO:0030136clathrin-coated vesicle0.0447778552108827



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>disease_data<br>


Cell Type
Ontology termp-valuen
neuronal stem cell5.48e-088
Uber Anatomy
Ontology termp-valuen
regional part of nervous system6.51e-5294
nervous system6.51e-5294
central nervous system3.18e-5082
neural tube7.09e-4657
neural rod7.09e-4657
future spinal cord7.09e-4657
neural keel7.09e-4657
adult organism3.77e-41115
neurectoderm4.68e-3990
brain4.70e-3969
future brain4.70e-3969
regional part of forebrain2.89e-3841
forebrain2.89e-3841
future forebrain2.89e-3841
regional part of brain9.13e-3859
anterior neural tube6.18e-3742
neural plate2.12e-3686
presumptive neural plate2.12e-3686
telencephalon1.71e-3134
gray matter1.80e-3134
brain grey matter1.80e-3134
regional part of telencephalon1.79e-3033
cerebral hemisphere3.77e-3032
pre-chordal neural plate5.87e-2861
ectoderm4.89e-27173
presumptive ectoderm4.89e-27173
ectoderm-derived structure6.43e-25169
cerebral cortex1.01e-2325
pallium1.01e-2325
regional part of cerebral cortex4.22e-2322
neocortex2.31e-2120
anterior region of body5.92e-20129
craniocervical region5.92e-20129
head3.75e-19123
tube7.14e-12194
embryo1.66e-10612
posterior neural tube5.03e-1015
chordal neural plate5.03e-1015
basal ganglion2.92e-099
nuclear complex of neuraxis2.92e-099
aggregate regional part of brain2.92e-099
collection of basal ganglia2.92e-099
cerebral subcortex2.92e-099
nucleus of brain3.92e-099
neural nucleus3.92e-099
temporal lobe9.76e-097
anatomical conduit2.04e-08241
segmental subdivision of nervous system2.24e-0813
embryonic structure2.75e-08605
developing anatomical structure2.75e-08605
diencephalon4.17e-087
future diencephalon4.17e-087
organ4.55e-08511
germ layer5.30e-08604
embryonic tissue5.30e-08604
presumptive structure5.30e-08604
epiblast (generic)5.30e-08604
segmental subdivision of hindbrain1.04e-0712
hindbrain1.04e-0712
presumptive hindbrain1.04e-0712
multi-cellular organism1.27e-07659
telencephalic nucleus1.93e-077
gyrus2.34e-076
Disease
Ontology termp-valuen
neuroectodermal tumor7.55e-0910


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


(#promoters = Number of promoters in this coexpression cluster that have ChIP signal of the TF)

TF#promotersEnrichmentp-valueq-value
CTCF#1066494.38566430524321.04204760534736e-050.000270857167383953
RAD21#588598.472300459918813.34431965405885e-082.24039384445319e-06
REST#5978119.650028716128021.47593496597899e-111.80709462968206e-09
SIN3A#2594273.442017553427810.001206753943353430.00818284476625688
TBP#690893.032812380351590.0002388258630576910.00260063959043709
YY1#752873.125290477179730.002193839507732880.0126447243017723
ZNF263#10127107.474401488191526.91943485229632e-095.40103779177112e-07



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.