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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
-
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>cell_data<br>uberon_data<br><br>


Cell Type
Ontology termp-valuen
adult endothelial progenitor cell1.53e-073
Uber Anatomy
Ontology termp-valuen
adult organism6.48e-83114
neural tube1.06e-3956
neural rod1.06e-3956
future spinal cord1.06e-3956
neural keel1.06e-3956
regional part of nervous system6.07e-3553
regional part of brain6.07e-3553
regional part of forebrain2.04e-2841
forebrain2.04e-2841
anterior neural tube2.04e-2841
future forebrain2.04e-2841
neural plate2.27e-2882
presumptive neural plate2.27e-2882
central nervous system3.34e-2881
neurectoderm5.94e-2886
brain3.41e-2668
future brain3.41e-2668
nervous system7.12e-2689
brain grey matter3.16e-2534
gray matter3.16e-2534
telencephalon4.54e-2534
regional part of telencephalon5.49e-2232
cerebral hemisphere7.76e-2232
ecto-epithelium6.56e-21104
organ system subdivision1.16e-19223
pre-chordal neural plate1.42e-1961
regional part of cerebral cortex3.68e-1722
structure with developmental contribution from neural crest6.06e-17132
neocortex1.45e-1620
cerebral cortex1.16e-1425
pallium1.16e-1425
tube2.24e-13192
neural nucleus3.41e-139
nucleus of brain3.41e-139
brainstem6.01e-136
posterior neural tube3.26e-1215
chordal neural plate3.26e-1215
ectoderm-derived structure4.38e-12171
ectoderm4.38e-12171
presumptive ectoderm4.38e-12171
anatomical conduit1.51e-11240
anatomical cluster1.72e-11373
organ2.02e-10503
multi-tissue structure5.68e-10342
basal ganglion1.39e-099
nuclear complex of neuraxis1.39e-099
aggregate regional part of brain1.39e-099
collection of basal ganglia1.39e-099
cerebral subcortex1.39e-099
telencephalic nucleus1.67e-097
segmental subdivision of nervous system2.76e-0913
developing anatomical structure7.61e-08581
segmental subdivision of hindbrain1.01e-0712
hindbrain1.01e-0712
presumptive hindbrain1.01e-0712
embryo1.02e-07592
germ layer1.13e-07560
germ layer / neural crest1.13e-07560
embryonic tissue1.13e-07560
presumptive structure1.13e-07560
germ layer / neural crest derived structure1.13e-07560
epiblast (generic)1.13e-07560
gyrus1.80e-076
embryonic structure1.85e-07564
pons2.35e-073
medulla oblongata3.00e-073
myelencephalon3.00e-073
future myelencephalon3.00e-073
spinal cord4.56e-073
dorsal region element4.56e-073
dorsum4.56e-073
epithelium6.84e-07306
organ part7.18e-07218
multi-cellular organism7.47e-07656


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.