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Coexpression cluster:C2506

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Full id: C2506_putamen_caudate_nucleus_temporal_amygdala_insula_frontal



Phase1 CAGE Peaks

Hg19::chr19:7989858..7989889,-p2@CTXN1
Hg19::chr19:7990008..7990044,-p4@CTXN1
Hg19::chr19:7990260..7990308,+p@chr19:7990260..7990308
+
Hg19::chr19:7990991..7991059,-p1@CTXN1


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>


Cell Type
Ontology termp-valuen
embryonic cell9.71e-18248
epithelial cell2.58e-16254
neurectodermal cell1.01e-1159
lining cell5.61e-1157
barrier cell5.61e-1157
mesodermal cell8.22e-11119
ectodermal cell2.59e-1071
neural cell2.01e-0825
squamous epithelial cell3.63e-0862
meso-epithelial cell1.04e-0744
migratory neural crest cell5.31e-0741
Uber Anatomy
Ontology termp-valuen
regional part of nervous system5.24e-2594
nervous system5.24e-2594
central nervous system2.60e-2482
cell layer1.39e-21312
neurectoderm1.79e-2190
epithelium2.72e-21309
pre-chordal neural plate1.42e-2061
neural plate2.33e-2086
presumptive neural plate2.33e-2086
anatomical cluster6.00e-20286
brain6.76e-2069
future brain6.76e-2069
tube9.01e-20194
regional part of forebrain4.77e-1941
forebrain4.77e-1941
future forebrain4.77e-1941
telencephalon5.56e-1934
cerebral hemisphere6.51e-1932
gray matter9.42e-1934
brain grey matter9.42e-1934
anatomical conduit1.23e-18241
regional part of telencephalon2.23e-1833
anterior neural tube3.41e-1842
neural tube6.85e-1857
neural rod6.85e-1857
future spinal cord6.85e-1857
neural keel6.85e-1857
ectoderm1.50e-17173
presumptive ectoderm1.50e-17173
regional part of brain1.28e-1659
ectoderm-derived structure1.51e-16169
head2.32e-15123
organism subdivision4.57e-15365
multi-tissue structure6.98e-15347
cerebral cortex1.27e-1425
pallium1.27e-1425
anterior region of body2.79e-13129
craniocervical region2.79e-13129
regional part of cerebral cortex2.88e-1322
embryo4.03e-12612
neocortex4.77e-1220
organ part2.84e-11219
multi-cellular organism7.41e-11659
embryonic structure1.46e-10605
developing anatomical structure1.46e-10605
germ layer2.48e-10604
embryonic tissue2.48e-10604
presumptive structure2.48e-10604
epiblast (generic)2.48e-10604
intermediate mesoderm2.08e-0837
vasculature5.61e-0879
vascular system5.61e-0879
anatomical system9.87e-08625
anatomical group1.41e-07626
squamous epithelium1.82e-0725
artery3.26e-0742
arterial blood vessel3.26e-0742
arterial system3.26e-0742
simple squamous epithelium6.08e-0722
urinary system structure7.15e-0744
blood vessel7.23e-0760
epithelial tube open at both ends7.23e-0760
blood vasculature7.23e-0760
vascular cord7.23e-0760


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
CCNT2#90546.336201576962630.0006203100587215640.00512211908782586
CTCFL#140690314.80985576923080.0004996291767563340.00440939425310586
E2F4#187439.501045236463330.001850751034728270.0109283986722443
MAX#414934.839416631755340.01315737137836840.0466221995448671
NANOG#79923214.62238924050630.006698757715363760.0284916129926644
NRF1#4899412.21027944771094.49717228915276e-050.00079391510599531
PAX5#507935.002174148383370.01196533174786410.043494736779617
RAD21#588537.766275421592250.0033411193858720.0172684301252579
SETDB1#9869330.24001963350795.98509618524166e-050.000984684090249612
SMC3#9126311.28369963369960.001115802366868050.00765709201612016
ZBTB7A#5134147.35190930787590.000342223540015990.00346600895032292
ZNF143#7702310.12565741417090.001534861610688180.0097666125485081



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.