Coexpression cluster:C4660

Full id: C4660_lung_cerebellum_rhabdomyosarcoma_mesenchymal_Neural_myxofibrosarcoma_Fibroblast

Phase1 CAGE Peaks

Hg19::chr7:14029034..14029087,-	p5@ETV1
Hg19::chr7:14029283..14029311,-	p1@ETV1
Hg19::chr7:14029312..14029325,-	p4@ETV1

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	1.57e-19	180
fibroblast	2.30e-08	75
electrically responsive cell	3.85e-08	60
electrically active cell	3.85e-08	60
muscle precursor cell	4.10e-07	57
myoblast	4.10e-07	57
multi-potent skeletal muscle stem cell	4.10e-07	57
neurectodermal cell	6.10e-07	59

Uber Anatomy

Ontology term	p-value	n
organism subdivision	1.87e-30	365
multi-tissue structure	3.32e-29	347
central nervous system	1.49e-26	82
regional part of nervous system	2.67e-26	94
nervous system	2.67e-26	94
ectoderm-derived structure	8.58e-25	169
anatomical cluster	2.31e-24	286
cell layer	5.01e-24	312
head	1.03e-23	123
ectoderm	1.31e-23	173
presumptive ectoderm	1.31e-23	173
epithelium	3.62e-23	309
anterior region of body	5.92e-23	129
craniocervical region	5.92e-23	129
neural plate	6.23e-23	86
presumptive neural plate	6.23e-23	86
neural tube	1.81e-22	57
neural rod	1.81e-22	57
future spinal cord	1.81e-22	57
neural keel	1.81e-22	57
brain	4.00e-22	69
future brain	4.00e-22	69
regional part of brain	4.74e-22	59
neurectoderm	3.98e-21	90
anatomical conduit	2.39e-19	241
tube	8.63e-19	194
pre-chordal neural plate	1.60e-18	61
regional part of forebrain	4.19e-18	41
forebrain	4.19e-18	41
future forebrain	4.19e-18	41
anterior neural tube	5.40e-18	42
multi-cellular organism	6.21e-17	659
telencephalon	8.14e-16	34
cerebral hemisphere	1.55e-15	32
gray matter	1.93e-15	34
brain grey matter	1.93e-15	34
regional part of telencephalon	3.32e-15	33
anatomical system	5.41e-15	625
anatomical group	7.77e-15	626
adult organism	9.91e-15	115
embryo	8.62e-14	612
regional part of cerebral cortex	4.84e-13	22
cerebral cortex	1.92e-12	25
pallium	1.92e-12	25
neocortex	6.49e-12	20
embryonic structure	8.58e-12	605
developing anatomical structure	8.58e-12	605
germ layer	1.47e-11	604
embryonic tissue	1.47e-11	604
presumptive structure	1.47e-11	604
epiblast (generic)	1.47e-11	604
organ part	3.90e-10	219
somite	1.09e-09	83
paraxial mesoderm	1.09e-09	83
presomitic mesoderm	1.09e-09	83
presumptive segmental plate	1.09e-09	83
trunk paraxial mesoderm	1.09e-09	83
presumptive paraxial mesoderm	1.09e-09	83
organ	2.26e-09	511
primordium	5.96e-09	168
dermomyotome	6.72e-09	70
mesenchyme	7.53e-08	238
entire embryonic mesenchyme	7.53e-08	238
trunk	4.47e-07	216

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
CEBPB#1051	3	7.97114762582482	0.00197418705528856	0.0115787118474354
CTCF#10664	3	5.36025637307503	0.006492509252767	0.0281228971776257
CTCFL#140690	3	19.7464743589744	0.000129837200555116	0.00172322625349801
EP300#2033	3	6.7739417262232	0.00321688050010379	0.0168430231388349
GATA2#2624	3	12.744931733554	0.000482952770428379	0.00438944429473236
RAD21#5885	3	10.3550338954563	0.000900491207356542	0.00668417919012863
SP1#6667	3	5.6983813781409	0.00540396270171217	0.0247841410769417
SPI1#6688	3	8.20432350852273	0.00181059318941052	0.0109411874158911

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.