Coexpression cluster:C1943

Full id: C1943_extraskeletal_temporal_occipital_adrenal_parietal_duodenum_bone

Phase1 CAGE Peaks

Hg19::chr4:66460864..66460869,-	p@chr4:66460864..66460869 -
Hg19::chr4:66536057..66536071,-	p5@EPHA5
Hg19::chr4:66536169..66536189,-	p1@EPHA5
Hg19::chr4:66536196..66536216,-	p2@EPHA5
Hg19::chr4:66536221..66536236,-	p4@EPHA5

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
non-terminally differentiated cell	7.40e-18	180
vascular associated smooth muscle cell	4.15e-10	32
smooth muscle cell	1.19e-09	42
smooth muscle myoblast	1.19e-09	42
neurectodermal cell	3.80e-09	59
electrically responsive cell	2.12e-08	60
electrically active cell	2.12e-08	60
migratory neural crest cell	1.29e-07	41
muscle precursor cell	2.07e-07	57
myoblast	2.07e-07	57
multi-potent skeletal muscle stem cell	2.07e-07	57
contractile cell	3.97e-07	59
muscle cell	4.07e-07	54

Uber Anatomy

Ontology term	p-value	n
regional part of nervous system	7.97e-34	94
nervous system	7.97e-34	94
central nervous system	2.19e-32	82
neural plate	1.01e-31	86
presumptive neural plate	1.01e-31	86
neural tube	2.08e-30	57
neural rod	2.08e-30	57
future spinal cord	2.08e-30	57
neural keel	2.08e-30	57
neurectoderm	2.83e-30	90
brain	5.03e-27	69
future brain	5.03e-27	69
regional part of brain	8.91e-27	59
ectoderm-derived structure	1.10e-25	169
ectoderm	4.45e-25	173
presumptive ectoderm	4.45e-25	173
regional part of forebrain	3.36e-23	41
forebrain	3.36e-23	41
future forebrain	3.36e-23	41
anterior neural tube	4.72e-23	42
pre-chordal neural plate	1.56e-21	61
head	3.36e-21	123
anterior region of body	3.39e-20	129
craniocervical region	3.39e-20	129
gray matter	4.64e-20	34
brain grey matter	4.64e-20	34
tube	5.25e-20	194
telencephalon	8.46e-20	34
cerebral hemisphere	2.05e-19	32
regional part of telencephalon	3.24e-19	33
epithelium	7.07e-19	309
cell layer	1.73e-18	312
organism subdivision	2.94e-17	365
multi-tissue structure	2.02e-16	347
cerebral cortex	2.35e-16	25
pallium	2.35e-16	25
regional part of cerebral cortex	1.09e-15	22
anatomical conduit	1.15e-15	241
adult organism	1.64e-15	115
anatomical cluster	4.14e-15	286
neocortex	2.25e-14	20
embryo	1.95e-11	612
embryonic structure	2.56e-11	605
developing anatomical structure	2.56e-11	605
germ layer	4.51e-11	604
embryonic tissue	4.51e-11	604
presumptive structure	4.51e-11	604
epiblast (generic)	4.51e-11	604
multi-cellular organism	2.11e-09	659
organ part	5.15e-09	219
anatomical system	1.34e-08	625
posterior neural tube	1.85e-08	15
chordal neural plate	1.85e-08	15
artery	1.88e-08	42
arterial blood vessel	1.88e-08	42
arterial system	1.88e-08	42
anatomical group	1.98e-08	626
systemic artery	6.15e-08	33
systemic arterial system	6.15e-08	33
skeletal muscle tissue	2.53e-07	61
striated muscle tissue	2.53e-07	61
myotome	2.53e-07	61
muscle tissue	2.58e-07	63
musculature	2.58e-07	63
musculature of body	2.58e-07	63
somite	4.13e-07	83
paraxial mesoderm	4.13e-07	83
presomitic mesoderm	4.13e-07	83
presumptive segmental plate	4.13e-07	83
trunk paraxial mesoderm	4.13e-07	83
presumptive paraxial mesoderm	4.13e-07	83
splanchnic layer of lateral plate mesoderm	6.01e-07	84

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
CTCF#10664	4	4.28820509846002	0.00515201558824328	0.0239440795665957
E2F1#1869	4	3.92591137190346	0.00721498454710636	0.0298816580527121
E2F6#1876	4	4.01372458535791	0.00663211823393388	0.0283038491432584
FOS#2353	4	7.19836424711553	0.000694785845338251	0.00559854478059421
RAD21#5885	4	8.28402711636506	0.000401162263912245	0.00386931895832388
TRIM28#10155	4	14.87242003621	4.00368496902357e-05	0.000734869691528739
ZNF263#10127	4	6.57747330960854	0.000987510323790016	0.00709462686292258

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.