Coexpression cluster:C4573

Full id: C4573_Melanocyte_Monocytederived_Osteoblast_Alveolar_Smooth_mesothelioma_Hepatic

Phase1 CAGE Peaks

Hg19::chr6:146864862..146864881,+	p3@RAB32
Hg19::chr6:146864935..146864949,+	p2@RAB32
Hg19::chr6:146864960..146864999,+	p1@RAB32

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

---

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>

---

Cell Type

Ontology term	p-value	n
somatic cell	2.34e-37	588
animal cell	1.61e-30	679
eukaryotic cell	1.61e-30	679
mesodermal cell	1.90e-23	121
granulocyte monocyte progenitor cell	2.00e-21	67
myeloid leukocyte	3.72e-21	72
embryonic cell	1.58e-20	250
native cell	2.36e-20	722
defensive cell	6.15e-20	48
phagocyte	6.15e-20	48
macrophage dendritic cell progenitor	1.23e-19	61
monopoietic cell	2.31e-19	59
monocyte	2.31e-19	59
monoblast	2.31e-19	59
promonocyte	2.31e-19	59
myeloid lineage restricted progenitor cell	4.52e-19	66
classical monocyte	5.37e-18	42
CD14-positive, CD16-negative classical monocyte	5.37e-18	42
stuff accumulating cell	1.37e-17	87
contractile cell	1.72e-14	59
muscle cell	7.50e-14	55
smooth muscle cell	1.02e-13	43
smooth muscle myoblast	1.02e-13	43
muscle precursor cell	2.07e-13	58
myoblast	2.07e-13	58
multi-potent skeletal muscle stem cell	2.07e-13	58
multi fate stem cell	9.87e-13	427
somatic stem cell	2.10e-12	433
stem cell	5.16e-12	441
non-terminally differentiated cell	9.44e-11	106
myeloid cell	1.70e-10	108
common myeloid progenitor	1.70e-10	108
vascular associated smooth muscle cell	2.72e-10	32
lining cell	3.18e-10	58
barrier cell	3.18e-10	58
electrically responsive cell	5.77e-10	61
electrically active cell	5.77e-10	61
meso-epithelial cell	3.44e-09	45
endothelial cell	3.56e-09	36
columnar/cuboidal epithelial cell	1.07e-07	27
epithelial cell	4.57e-07	253

Uber Anatomy

Ontology term	p-value	n
lateral plate mesoderm	1.82e-32	203
mesoderm	5.59e-31	315
mesoderm-derived structure	5.59e-31	315
presumptive mesoderm	5.59e-31	315
musculoskeletal system	2.52e-30	167
bone marrow	3.45e-21	76
skeletal element	1.27e-19	90
bone element	1.98e-19	82
skeletal system	1.97e-18	100
immune system	1.46e-17	93
epithelial tube	1.02e-15	117
hemolymphoid system	3.79e-15	108
epithelial vesicle	5.28e-15	78
hematopoietic system	1.62e-14	98
blood island	1.62e-14	98
vasculature	6.13e-14	78
vascular system	6.13e-14	78
unilaminar epithelium	6.28e-14	148
anatomical system	1.13e-13	624
cardiovascular system	1.53e-13	109
anatomical group	2.46e-13	625
splanchnic layer of lateral plate mesoderm	2.84e-13	83
somite	7.26e-13	71
presomitic mesoderm	7.26e-13	71
presumptive segmental plate	7.26e-13	71
dermomyotome	7.26e-13	71
trunk paraxial mesoderm	7.26e-13	71
developing anatomical structure	8.74e-13	581
dense mesenchyme tissue	1.21e-12	73
trunk mesenchyme	1.67e-12	122
multilaminar epithelium	1.83e-12	83
circulatory system	1.98e-12	112
paraxial mesoderm	2.35e-12	72
presumptive paraxial mesoderm	2.35e-12	72
vessel	8.34e-12	68
multi-cellular organism	9.43e-12	656
embryonic structure	9.88e-12	564
embryo	1.24e-11	592
skeletal muscle tissue	1.83e-11	62
striated muscle tissue	1.83e-11	62
myotome	1.83e-11	62
artery	2.00e-11	42
arterial blood vessel	2.00e-11	42
arterial system	2.00e-11	42
mesenchyme	2.22e-11	160
entire embryonic mesenchyme	2.22e-11	160
epithelial tube open at both ends	2.44e-11	59
blood vessel	2.44e-11	59
blood vasculature	2.44e-11	59
vascular cord	2.44e-11	59
germ layer	4.98e-11	560
germ layer / neural crest	4.98e-11	560
embryonic tissue	4.98e-11	560
presumptive structure	4.98e-11	560
germ layer / neural crest derived structure	4.98e-11	560
epiblast (generic)	4.98e-11	560
muscle tissue	6.90e-11	64
musculature	6.90e-11	64
musculature of body	6.90e-11	64

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
CCNT2#905	3	6.33620157696263	0.00393075003576489	0.0190967857368586
CTCF#10664	3	5.36025637307503	0.006492509252767	0.0281077422421544
CTCFL#140690	3	19.7464743589744	0.000129837200555116	0.00172256953617579
E2F1#1869	3	4.90738921487932	0.00846098534723939	0.0327377315011979
E2F6#1876	3	5.01715573169739	0.0079176980688633	0.0324026829394206
ELF1#1997	3	4.25809795880754	0.0129517987505461	0.0464596568678785
GABPB1#2553	3	7.06768383618217	0.00283221282541742	0.0154727977859377
HMGN3#9324	3	8.17854772335059	0.00182776694216421	0.0109105024961527
HNF4A#3172	3	23.1322903629537	8.07584663437677e-05	0.00123345034607733
RAD21#5885	3	10.3550338954563	0.000900491207356542	0.00667990632893741
SMC3#9126	3	15.0449328449328	0.000293582542037187	0.00310590225970641
SPI1#6688	3	8.20432350852273	0.00181059318941052	0.0109373903701108
TAF7#6879	3	11.4330694049239	0.000669018198194583	0.00545275414400219
USF1#7391	3	6.36149927720796	0.0038840405729056	0.0191035750868272
ZBTB7A#51341	3	7.3519093078759	0.00251625586028227	0.0140795738436657

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.