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Coexpression cluster:C3287

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Full id: C3287_Wilms_brain_duodenum_occipital_temporal_cerebellum_parietal



Phase1 CAGE Peaks

Hg19::chr12:50451133..50451188,+p2@ACCN2
Hg19::chr12:50451363..50451429,+p1@ACCN2
Hg19::chr19:36359341..36359352,+p6@APLP1


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:0009268response to pH0.0202716415057658
GO:0006378mRNA polyadenylation0.0202716415057658
GO:0015280amiloride-sensitive sodium channel activity0.0202716415057658
GO:0043631RNA polyadenylation0.0202716415057658
GO:0031124mRNA 3'-end processing0.0202716415057658
GO:0031123RNA 3'-end processing0.0229245737102913
GO:0005905coated pit0.0369863583011517
GO:0030198extracellular matrix organization and biogenesis0.0369863583011517
GO:0030900forebrain development0.0369863583011517
GO:0005272sodium channel activity0.0412411474532464
GO:0005604basement membrane0.0427872738164806
GO:0008201heparin binding0.0427872738164806
GO:0044459plasma membrane part0.0427872738164806
GO:0043062extracellular structure organization and biogenesis0.0433944682033477
GO:0031402sodium ion binding0.0462792474072028
GO:0005539glycosaminoglycan binding0.0469878124796556
GO:0030247polysaccharide binding0.0469878124796556
GO:0005507copper ion binding0.0469878124796556
GO:0001871pattern binding0.04733948380619
GO:0044420extracellular matrix part0.04733948380619
GO:0007420brain development0.047832875049538
GO:0015276ligand-gated ion channel activity0.0478936926355097
GO:0022834ligand-gated channel activity0.0478936926355097
GO:0009628response to abiotic stimulus0.0478936926355097
GO:0006814sodium ion transport0.0478936926355097
GO:0006816calcium ion transport0.0478936926355097
GO:0006417regulation of translation0.0478936926355097
GO:0010324membrane invagination0.0478936926355097
GO:0006897endocytosis0.0478936926355097
GO:0031326regulation of cellular biosynthetic process0.0478936926355097
GO:0005886plasma membrane0.0485554587584505
GO:0009889regulation of biosynthetic process0.0485554587584505
GO:0031420alkali metal ion binding0.0485554587584505
GO:0007417central nervous system development0.0492402134427232
GO:0006810transport0.0492402134427232
GO:0015674di-, tri-valent inorganic cation transport0.0492402134427232
GO:0051234establishment of localization0.0492402134427232



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>


Cell Type
Ontology termp-valuen
non-terminally differentiated cell1.50e-07180
Uber Anatomy
Ontology termp-valuen
regional part of nervous system1.11e-3294
nervous system1.11e-3294
central nervous system7.09e-3182
brain7.03e-2869
future brain7.03e-2869
neural tube2.79e-2557
neural rod2.79e-2557
future spinal cord2.79e-2557
neural keel2.79e-2557
neural plate1.11e-2486
presumptive neural plate1.11e-2486
neurectoderm1.13e-2490
ectoderm1.13e-23173
presumptive ectoderm1.13e-23173
ectoderm-derived structure2.19e-23169
regional part of brain2.94e-2359
organism subdivision4.51e-23365
head1.06e-21123
anterior region of body6.34e-21129
craniocervical region6.34e-21129
telencephalon4.92e-2034
gray matter5.47e-2034
brain grey matter5.47e-2034
multi-tissue structure8.84e-20347
regional part of telencephalon2.20e-1933
cerebral hemisphere7.55e-1932
regional part of forebrain7.78e-1841
forebrain7.78e-1841
future forebrain7.78e-1841
pre-chordal neural plate2.40e-1761
epithelium3.66e-17309
cell layer4.85e-17312
anterior neural tube5.15e-1742
regional part of cerebral cortex1.14e-1422
cerebral cortex1.40e-1425
pallium1.40e-1425
neocortex1.48e-1320
organ part1.66e-13219
tube1.50e-10194
embryo8.03e-10612
posterior neural tube1.23e-0915
chordal neural plate1.23e-0915
embryonic structure1.83e-09605
developing anatomical structure1.83e-09605
anatomical cluster2.20e-09286
organ segment2.53e-0997
germ layer3.13e-09604
embryonic tissue3.13e-09604
presumptive structure3.13e-09604
epiblast (generic)3.13e-09604
segmental subdivision of nervous system1.40e-0813
multi-cellular organism1.60e-08659
organ2.24e-08511
anatomical system2.49e-08625
anatomical group4.37e-08626
anatomical conduit4.94e-08241
segmental subdivision of hindbrain5.52e-0812
hindbrain5.52e-0812
presumptive hindbrain5.52e-0812
basal ganglion5.94e-079
nuclear complex of neuraxis5.94e-079
aggregate regional part of brain5.94e-079
collection of basal ganglia5.94e-079
cerebral subcortex5.94e-079
nucleus of brain6.73e-079
neural nucleus6.73e-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


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

TF#promotersEnrichmentp-valueq-value
E2F1#186934.907389214879320.008460985347239390.0324087452754469
ZNF263#1012738.221841637010680.001799043925565870.0109023064025864



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.