Coexpression cluster:C4126

Full id: C4126_salivary_astrocytoma_spinal_hippocampus_medulla_thalamus_amygdala

Phase1 CAGE Peaks

Hg19::chr2:131594446..131594472,+	p3@ARHGEF4
Hg19::chr2:131594478..131594502,+	p2@ARHGEF4
Hg19::chr2:131594505..131594522,+	p5@ARHGEF4

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>cell_data<br>uberon_data<br>disease_data<br>

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Cell Type

Ontology term	p-value	n
epithelial cell	5.22e-19	254
endo-epithelial cell	9.35e-14	43
endodermal cell	2.07e-10	59
respiratory epithelial cell	3.88e-07	13
epithelial cell of alimentary canal	6.84e-07	21

Uber Anatomy

Ontology term	p-value	n
regional part of nervous system	2.62e-33	94
nervous system	2.62e-33	94
central nervous system	4.39e-33	82
neural tube	6.75e-33	57
neural rod	6.75e-33	57
future spinal cord	6.75e-33	57
neural keel	6.75e-33	57
ectoderm	2.80e-32	173
presumptive ectoderm	2.80e-32	173
ectoderm-derived structure	1.61e-31	169
head	6.13e-28	123
brain	9.51e-28	69
future brain	9.51e-28	69
anterior region of body	9.82e-28	129
craniocervical region	9.82e-28	129
regional part of brain	1.44e-25	59
regional part of forebrain	7.58e-25	41
forebrain	7.58e-25	41
future forebrain	7.58e-25	41
neurectoderm	1.11e-24	90
neural plate	4.12e-24	86
presumptive neural plate	4.12e-24	86
anterior neural tube	9.15e-24	42
gray matter	1.49e-21	34
brain grey matter	1.49e-21	34
telencephalon	1.85e-21	34
regional part of telencephalon	7.32e-21	33
cerebral hemisphere	6.28e-20	32
adult organism	5.72e-19	115
pre-chordal neural plate	5.40e-18	61
organ part	2.73e-15	219
cerebral cortex	3.22e-15	25
pallium	3.22e-15	25
embryo	5.60e-15	612
organ	5.71e-15	511
regional part of cerebral cortex	5.95e-14	22
embryonic structure	1.27e-12	605
developing anatomical structure	1.27e-12	605
neocortex	1.87e-12	20
germ layer	2.65e-12	604
embryonic tissue	2.65e-12	604
presumptive structure	2.65e-12	604
epiblast (generic)	2.65e-12	604
respiratory system	2.79e-12	72
organism subdivision	3.16e-12	365
endoderm-derived structure	7.20e-12	169
endoderm	7.20e-12	169
presumptive endoderm	7.20e-12	169
multi-tissue structure	1.39e-11	347
multi-cellular organism	2.01e-11	659
digestive system	8.35e-11	155
digestive tract	8.35e-11	155
primitive gut	8.35e-11	155
anatomical cluster	1.45e-10	286
anatomical conduit	2.75e-10	241
posterior neural tube	3.46e-10	15
chordal neural plate	3.46e-10	15
anatomical system	3.66e-10	625
anatomical group	5.16e-10	626
foregut	8.30e-10	98
anatomical space	2.31e-09	104
respiratory tract	2.32e-09	53
subdivision of digestive tract	3.21e-09	129
endodermal part of digestive tract	3.21e-09	129
segment of respiratory tract	5.15e-09	46
mixed endoderm/mesoderm-derived structure	1.65e-08	130
respiratory primordium	3.23e-08	38
endoderm of foregut	3.23e-08	38
segmental subdivision of nervous system	3.79e-08	13
nucleus of brain	7.07e-08	9
neural nucleus	7.07e-08	9
segmental subdivision of hindbrain	8.30e-08	12
hindbrain	8.30e-08	12
presumptive hindbrain	8.30e-08	12
basal ganglion	1.01e-07	9
nuclear complex of neuraxis	1.01e-07	9
aggregate regional part of brain	1.01e-07	9
collection of basal ganglia	1.01e-07	9
cerebral subcortex	1.01e-07	9
organ segment	1.26e-07	97
primordium	1.83e-07	168
immaterial anatomical entity	3.62e-07	126
tube	7.30e-07	194

Disease

Ontology term	p-value	n
carcinoma	2.32e-18	106
cell type cancer	1.56e-15	143
cancer	2.86e-08	235
disease of cellular proliferation	4.15e-08	239
squamous cell carcinoma	2.80e-07	14

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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No analysis results for this cluster

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.