Coexpression cluster:C1192

Full id: C1192_extraskeletal_Cardiac_Lens_cholangiocellular_pineal_Fibroblast_rectum

Phase1 CAGE Peaks

Hg19::chr13:93879041..93879078,+	p1@GPC6
Hg19::chr13:93879085..93879136,+	p2@GPC6
Hg19::chr13:93879137..93879148,+	p10@GPC6
Hg19::chr13:93879165..93879189,+	p3@GPC6
Hg19::chr13:93879196..93879223,+	p4@GPC6
Hg19::chr13:93879225..93879248,+	p9@GPC6
Hg19::chr13:93879313..93879326,+	p7@GPC6

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	1.04e-26	180
fibroblast	1.63e-12	75
electrically responsive cell	1.09e-09	60
electrically active cell	1.09e-09	60
muscle precursor cell	8.53e-09	57
myoblast	8.53e-09	57
multi-potent skeletal muscle stem cell	8.53e-09	57
muscle cell	1.66e-08	54
contractile cell	3.63e-08	59
neural cell	3.70e-07	25

Uber Anatomy

Ontology term	p-value	n
organism subdivision	2.12e-26	365
multi-tissue structure	4.28e-20	347
cell layer	4.54e-16	312
epithelium	1.01e-15	309
trunk	1.27e-12	216
multi-cellular organism	1.08e-11	659
trunk mesenchyme	1.10e-11	143
regional part of nervous system	1.22e-11	94
nervous system	1.22e-11	94
tube	1.89e-10	194
central nervous system	4.19e-10	82
anatomical cluster	7.91e-10	286
ectoderm	1.39e-09	173
presumptive ectoderm	1.39e-09	173
neurectoderm	1.94e-09	90
anatomical conduit	3.74e-09	241
embryo	4.63e-09	612
ectoderm-derived structure	8.14e-09	169
muscle tissue	1.13e-08	63
musculature	1.13e-08	63
musculature of body	1.13e-08	63
skeletal muscle tissue	1.40e-08	61
striated muscle tissue	1.40e-08	61
myotome	1.40e-08	61
neural plate	1.47e-08	86
presumptive neural plate	1.47e-08	86
embryonic structure	3.60e-08	605
developing anatomical structure	3.60e-08	605
germ layer	6.55e-08	604
embryonic tissue	6.55e-08	604
presumptive structure	6.55e-08	604
epiblast (generic)	6.55e-08	604
head	6.87e-08	123
dermomyotome	8.26e-08	70
somite	1.11e-07	83
paraxial mesoderm	1.11e-07	83
presomitic mesoderm	1.11e-07	83
presumptive segmental plate	1.11e-07	83
trunk paraxial mesoderm	1.11e-07	83
presumptive paraxial mesoderm	1.11e-07	83
mesenchyme	1.18e-07	238
entire embryonic mesenchyme	1.18e-07	238
brain	1.71e-07	69
future brain	1.71e-07	69
anterior region of body	1.97e-07	129
craniocervical region	1.97e-07	129
abdominal segment of trunk	2.45e-07	61
abdomen	2.45e-07	61
subdivision of trunk	3.42e-07	113
pre-chordal neural plate	5.52e-07	61
anatomical system	8.41e-07	625
anatomical group	8.96e-07	626

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	7	44.8718135469774	2.71655591272133e-12	3.64671443404503e-10
EP300#2033	7	6.7739417262232	1.52695018318475e-06	5.85867561284469e-05
HEY1#23462	7	4.04011104310571	5.68979821988558e-05	0.000950018922920273
JUND#3727	7	6.99466394187103	1.21993360047445e-06	4.92495729802671e-05
MAX#4149	7	6.45255550900712	2.14589603858566e-06	7.76829242197047e-05
POLR2A#5430	7	2.14745317655807	0.00474763644761028	0.0223370755451829
RAD21#5885	7	10.3550338954563	7.82487927673307e-08	4.69668141829152e-06
REST#5978	7	9.65002871612802	1.28195528172884e-07	7.31618183980753e-06
RFX5#5993	7	12.0479108271951	2.7106444306642e-08	1.86003281007975e-06
SETDB1#9869	7	40.3200261780105	5.74662948954468e-12	7.45555574234232e-10
SP1#6667	7	5.6983813781409	5.12280185510121e-06	0.000157220188934739
TAF1#6872	7	3.34304628574529	0.000214233631962245	0.00246576441354474
TBP#6908	7	3.70677068709639	0.000103967209750511	0.00145085935584362
TRIM28#10155	7	18.5905250452625	1.300439693691e-09	1.17386880872424e-07
YY1#7528	7	4.91117074985386	1.45048003565243e-05	0.000345386877436169
ZNF263#10127	7	8.22184163701068	3.93423095812578e-07	1.90844006983603e-05

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.