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Coexpression cluster:C4021

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Full id: C4021_spinal_CD14_substantia_optic_medulla_locus_thalamus



Phase1 CAGE Peaks

Hg19::chr20:24951811..24951815,-p@chr20:24951811..24951815
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Hg19::chr5:42812123..42812140,-p10@SEPP1
Hg19::chr5:42812143..42812169,-p3@SEPP1


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
adult organism2.38e-72115
neural tube1.05e-3257
neural rod1.05e-3257
future spinal cord1.05e-3257
neural keel1.05e-3257
regional part of brain7.18e-2659
central nervous system2.92e-2482
anterior neural tube3.88e-2442
brain9.84e-2469
future brain9.84e-2469
regional part of forebrain2.19e-2341
forebrain2.19e-2341
future forebrain2.19e-2341
neurectoderm7.60e-2390
neural plate8.28e-2386
presumptive neural plate8.28e-2386
regional part of nervous system3.14e-2294
nervous system3.14e-2294
gray matter7.08e-1934
brain grey matter7.08e-1934
telencephalon7.84e-1934
regional part of telencephalon6.83e-1833
cerebral hemisphere8.29e-1732
anterior region of body1.15e-15129
craniocervical region1.15e-15129
pre-chordal neural plate1.92e-1561
head2.16e-14123
regional part of cerebral cortex1.07e-1322
ectoderm5.49e-13173
presumptive ectoderm5.49e-13173
ectoderm-derived structure1.07e-12169
organ4.18e-12511
neocortex5.04e-1220
cerebral cortex2.45e-1125
pallium2.45e-1125
brainstem4.15e-108
nucleus of brain8.60e-109
neural nucleus8.60e-109
posterior neural tube1.30e-0915
chordal neural plate1.30e-0915
basal ganglion3.00e-099
nuclear complex of neuraxis3.00e-099
aggregate regional part of brain3.00e-099
collection of basal ganglia3.00e-099
cerebral subcortex3.00e-099
segmental subdivision of nervous system6.49e-0813
telencephalic nucleus1.30e-077
multi-cellular organism2.33e-07659
embryo2.79e-07612
anatomical cluster3.09e-07286
segmental subdivision of hindbrain6.59e-0712
hindbrain6.59e-0712
presumptive hindbrain6.59e-0712
anatomical conduit8.77e-07241


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
BHLHE40#8553229.91454236465160.001467483527106140.00939799559035067
ESRRA#21012322.5602094240841.27639599649441e-050.000313144283481041
FOSL2#2355211.28680040304110.0100534586973120.0376793645621389
FOXA2#3170216.42030916844350.004810682352105480.0225940034254416
GATA3#2625218.15767757147070.003944546819279620.018953097407929
HNF4A#3172215.42152690863580.005444210486686610.0246772231682246
HNF4G#3174219.16894835096450.003543986611284220.0179736035398394
MAFF#23764237.54357099329680.0009344774015560320.00676996984885616
MAFK#7975218.06715542521990.003983674744936810.0191129642909985
RXRA#6256213.38307809275550.007196434429465730.0298332241249145
TRIM28#10155212.39368336350830.008368344129438470.0329183236359482



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.