Coexpression cluster:C4021

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

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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

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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>

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Uber Anatomy

Ontology term	p-value	n
adult organism	2.38e-72	115
neural tube	1.05e-32	57
neural rod	1.05e-32	57
future spinal cord	1.05e-32	57
neural keel	1.05e-32	57
regional part of brain	7.18e-26	59
central nervous system	2.92e-24	82
anterior neural tube	3.88e-24	42
brain	9.84e-24	69
future brain	9.84e-24	69
regional part of forebrain	2.19e-23	41
forebrain	2.19e-23	41
future forebrain	2.19e-23	41
neurectoderm	7.60e-23	90
neural plate	8.28e-23	86
presumptive neural plate	8.28e-23	86
regional part of nervous system	3.14e-22	94
nervous system	3.14e-22	94
gray matter	7.08e-19	34
brain grey matter	7.08e-19	34
telencephalon	7.84e-19	34
regional part of telencephalon	6.83e-18	33
cerebral hemisphere	8.29e-17	32
anterior region of body	1.15e-15	129
craniocervical region	1.15e-15	129
pre-chordal neural plate	1.92e-15	61
head	2.16e-14	123
regional part of cerebral cortex	1.07e-13	22
ectoderm	5.49e-13	173
presumptive ectoderm	5.49e-13	173
ectoderm-derived structure	1.07e-12	169
organ	4.18e-12	511
neocortex	5.04e-12	20
cerebral cortex	2.45e-11	25
pallium	2.45e-11	25
brainstem	4.15e-10	8
nucleus of brain	8.60e-10	9
neural nucleus	8.60e-10	9
posterior neural tube	1.30e-09	15
chordal neural plate	1.30e-09	15
basal ganglion	3.00e-09	9
nuclear complex of neuraxis	3.00e-09	9
aggregate regional part of brain	3.00e-09	9
collection of basal ganglia	3.00e-09	9
cerebral subcortex	3.00e-09	9
segmental subdivision of nervous system	6.49e-08	13
telencephalic nucleus	1.30e-07	7
multi-cellular organism	2.33e-07	659
embryo	2.79e-07	612
anatomical cluster	3.09e-07	286
segmental subdivision of hindbrain	6.59e-07	12
hindbrain	6.59e-07	12
presumptive hindbrain	6.59e-07	12
anatomical conduit	8.77e-07	241

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

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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

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

TF	#promoters	Enrichment	p-value	q-value
BHLHE40#8553	2	29.9145423646516	0.00146748352710614	0.00939799559035067
ESRRA#2101	2	322.560209424084	1.27639599649441e-05	0.000313144283481041
FOSL2#2355	2	11.2868004030411	0.010053458697312	0.0376793645621389
FOXA2#3170	2	16.4203091684435	0.00481068235210548	0.0225940034254416
GATA3#2625	2	18.1576775714707	0.00394454681927962	0.018953097407929
HNF4A#3172	2	15.4215269086358	0.00544421048668661	0.0246772231682246
HNF4G#3174	2	19.1689483509645	0.00354398661128422	0.0179736035398394
MAFF#23764	2	37.5435709932968	0.000934477401556032	0.00676996984885616
MAFK#7975	2	18.0671554252199	0.00398367474493681	0.0191129642909985
RXRA#6256	2	13.3830780927555	0.00719643442946573	0.0298332241249145
TRIM28#10155	2	12.3936833635083	0.00836834412943847	0.0329183236359482

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

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This analysis result is provided for C0 - C305 clusters.