Coexpression cluster:C538

Full id: C538_left_skeletal_heart_seminal_ductus_adipose_mature

Phase1 CAGE Peaks

Hg19::chr12:10856713..10856723,-	p23@CSDA
Hg19::chr17:58042483..58042495,+	p2@ENST00000501190 p2@uc002iye.1
Hg19::chr5:79026919..79026926,+	p@chr5:79026919..79026926 +
Hg19::chr5:79029312..79029328,+	p9@CMYA5
Hg19::chr7:95214018..95214046,-	p@chr7:95214018..95214046 -
Hg19::chr7:95218981..95219000,-	p12@PDK4
Hg19::chr7:95222151..95222232,-	p7@PDK4
Hg19::chr7:95223041..95223065,-	p@chr7:95223041..95223065 -
Hg19::chr7:95224363..95224402,-	p@chr7:95224363..95224402 -
Hg19::chr7:95224413..95224447,-	p@chr7:95224413..95224447 -
Hg19::chr7:95224469..95224481,-	p@chr7:95224469..95224481 -
Hg19::chr7:95225490..95225542,-	p3@PDK4
Hg19::chr7:95225580..95225618,-	p4@PDK4
Hg19::chr7:95225631..95225666,-	p2@PDK4
Hg19::chr7:95225695..95225721,-	p8@PDK4
Hg19::chr7:95225729..95225740,-	p6@PDK4
Hg19::chr7:95225768..95225967,-	p1@PDK4

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

---

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

---

GO ID	GO name	FDR corrected p-value
GO:0004740	pyruvate dehydrogenase (acetyl-transferring) kinase activity	0.0252486593058398
GO:0009409	response to cold	0.0252486593058398
GO:0018106	peptidyl-histidine phosphorylation	0.0252486593058398
GO:0018202	peptidyl-histidine modification	0.0252486593058398
GO:0004673	protein histidine kinase activity	0.0419458539477759
GO:0009266	response to temperature stimulus	0.0419458539477759
GO:0016775	phosphotransferase activity, nitrogenous group as acceptor	0.0419458539477759

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>

---

Cell Type

Ontology term	p-value	n
myeloid leukocyte	1.79e-09	76
classical monocyte	4.70e-08	45
macrophage dendritic cell progenitor	5.59e-08	65
granulocyte monocyte progenitor cell	5.76e-08	71
monopoietic cell	6.73e-08	63
monocyte	6.73e-08	63
monoblast	6.73e-08	63
promonocyte	6.73e-08	63
myeloid lineage restricted progenitor cell	1.51e-07	70
CD14-positive, CD16-negative classical monocyte	5.57e-07	42

Uber Anatomy

Ontology term	p-value	n
adult organism	5.93e-51	115
neural tube	2.15e-18	57
neural rod	2.15e-18	57
future spinal cord	2.15e-18	57
neural keel	2.15e-18	57
multi-cellular organism	3.04e-18	659
regional part of brain	2.72e-16	59
organ	4.95e-16	511
anatomical system	6.00e-16	625
anatomical group	1.28e-15	626
embryo	2.20e-15	612
anterior neural tube	4.85e-15	42
embryonic structure	1.08e-14	605
developing anatomical structure	1.08e-14	605
regional part of forebrain	1.98e-14	41
forebrain	1.98e-14	41
future forebrain	1.98e-14	41
germ layer	2.13e-14	604
embryonic tissue	2.13e-14	604
presumptive structure	2.13e-14	604
epiblast (generic)	2.13e-14	604
central nervous system	1.76e-13	82
brain	1.32e-12	69
future brain	1.32e-12	69
neural plate	1.86e-12	86
presumptive neural plate	1.86e-12	86
gray matter	1.19e-11	34
brain grey matter	1.19e-11	34
telencephalon	1.91e-11	34
regional part of telencephalon	3.60e-11	33
anatomical cluster	1.11e-10	286
neurectoderm	1.28e-10	90
cerebral hemisphere	1.51e-10	32
regional part of nervous system	3.49e-10	94
nervous system	3.49e-10	94
anatomical conduit	6.31e-10	241
tube	1.71e-09	194
hemolymphoid system	1.99e-09	112
immune system	8.61e-09	115
regional part of cerebral cortex	9.65e-09	22
hematopoietic system	1.19e-08	102
blood island	1.19e-08	102
pre-chordal neural plate	1.65e-08	61
mesoderm	3.04e-08	448
mesoderm-derived structure	3.04e-08	448
presumptive mesoderm	3.04e-08	448
neocortex	5.51e-08	20
cerebral cortex	6.68e-08	25
pallium	6.68e-08	25
multi-tissue structure	7.33e-08	347
bone marrow	3.40e-07	80
anterior region of body	5.11e-07	129
craniocervical region	5.11e-07	129
head	9.85e-07	123

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

---

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

---

(#promoters = Number of promoters in this coexpression cluster that have ChIP signal of the TF)

TF	#promoters	Enrichment	p-value	q-value
SMARCB1#6598	6	6.44213498158497	0.000197513604963961	0.00237323094671319
ZNF263#10127	6	2.90182646012142	0.0121295164888246	0.043984395422949

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

---

This analysis result is provided for C0 - C305 clusters.