Coexpression cluster:C2790

Full id: C2790_anaplastic_mesothelioma_corpus_optic_substantia_thalamus_granulosa

Phase1 CAGE Peaks

Hg19::chr4:41216492..41216550,-	p1@APBB2
Hg19::chr4:41216552..41216567,-	p2@APBB2
Hg19::chr4:41216580..41216594,-	p5@APBB2
Hg19::chr4:41216619..41216637,-	p3@APBB2

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><br>

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Cell Type

Ontology term	p-value	n
mesodermal cell	5.23e-15	119
non-terminally differentiated cell	3.58e-11	180
embryonic cell	1.68e-10	248
muscle precursor cell	5.72e-10	57
myoblast	5.72e-10	57
multi-potent skeletal muscle stem cell	5.72e-10	57
muscle cell	6.02e-09	54
contractile cell	2.40e-08	59
vascular associated smooth muscle cell	1.03e-07	32
smooth muscle cell	1.24e-07	42
smooth muscle myoblast	1.24e-07	42
squamous epithelial cell	4.75e-07	62
electrically responsive cell	5.26e-07	60
electrically active cell	5.26e-07	60

Uber Anatomy

Ontology term	p-value	n
cell layer	4.25e-30	312
epithelium	1.26e-29	309
organism subdivision	1.12e-27	365
anatomical cluster	8.02e-26	286
anatomical conduit	6.00e-25	241
tube	8.00e-24	194
multi-tissue structure	1.62e-21	347
multi-cellular organism	2.73e-18	659
neural plate	1.53e-16	86
presumptive neural plate	1.53e-16	86
vasculature	4.95e-16	79
vascular system	4.95e-16	79
head	4.29e-15	123
brain	4.44e-15	69
future brain	4.44e-15	69
regional part of brain	7.40e-15	59
neural tube	1.21e-14	57
neural rod	1.21e-14	57
future spinal cord	1.21e-14	57
neural keel	1.21e-14	57
anatomical system	1.45e-14	625
neurectoderm	1.69e-14	90
anatomical group	2.59e-14	626
anterior region of body	3.64e-14	129
craniocervical region	3.64e-14	129
ectoderm-derived structure	4.50e-14	169
embryo	1.04e-13	612
splanchnic layer of lateral plate mesoderm	1.23e-13	84
embryonic structure	1.98e-13	605
developing anatomical structure	1.98e-13	605
unilaminar epithelium	2.14e-13	138
central nervous system	2.92e-13	82
germ layer	3.91e-13	604
embryonic tissue	3.91e-13	604
presumptive structure	3.91e-13	604
epiblast (generic)	3.91e-13	604
vessel	4.97e-13	69
trunk	5.37e-13	216
blood vessel	7.37e-13	60
epithelial tube open at both ends	7.37e-13	60
blood vasculature	7.37e-13	60
vascular cord	7.37e-13	60
ectoderm	8.01e-13	173
presumptive ectoderm	8.01e-13	173
regional part of nervous system	9.49e-13	94
nervous system	9.49e-13	94
epithelial tube	5.67e-12	118
anterior neural tube	2.24e-11	42
pre-chordal neural plate	2.68e-11	61
regional part of forebrain	4.83e-11	41
forebrain	4.83e-11	41
future forebrain	4.83e-11	41
artery	6.96e-11	42
arterial blood vessel	6.96e-11	42
arterial system	6.96e-11	42
somite	1.31e-10	83
paraxial mesoderm	1.31e-10	83
presomitic mesoderm	1.31e-10	83
presumptive segmental plate	1.31e-10	83
trunk paraxial mesoderm	1.31e-10	83
presumptive paraxial mesoderm	1.31e-10	83
trunk mesenchyme	1.71e-10	143
cardiovascular system	3.87e-10	110
telencephalon	4.49e-10	34
gray matter	4.65e-10	34
brain grey matter	4.65e-10	34
circulatory system	5.37e-10	113
dermomyotome	9.77e-10	70
regional part of telencephalon	1.33e-09	33
skeletal muscle tissue	2.06e-09	61
striated muscle tissue	2.06e-09	61
myotome	2.06e-09	61
muscle tissue	3.29e-09	63
musculature	3.29e-09	63
musculature of body	3.29e-09	63
adult organism	4.61e-09	115
cerebral hemisphere	6.30e-09	32
systemic artery	2.52e-08	33
systemic arterial system	2.52e-08	33
organ part	4.88e-08	219
regional part of cerebral cortex	6.24e-08	22
organ	7.09e-08	511
mesenchyme	1.97e-07	238

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.