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

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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
somatic cell	3.84e-37	591
animal cell	4.77e-30	679
eukaryotic cell	4.77e-30	679
mesodermal cell	3.80e-23	119
granulocyte monocyte progenitor cell	6.13e-21	71
embryonic cell	1.63e-20	248
myeloid leukocyte	2.25e-20	76
native cell	2.12e-19	722
macrophage dendritic cell progenitor	4.68e-19	65
monopoietic cell	6.88e-19	63
monocyte	6.88e-19	63
monoblast	6.88e-19	63
promonocyte	6.88e-19	63
myeloid lineage restricted progenitor cell	1.06e-18	70
CD14-positive, CD16-negative classical monocyte	1.83e-18	42
classical monocyte	1.01e-16	45
contractile cell	3.23e-14	59
non-terminally differentiated cell	5.29e-14	180
smooth muscle cell	2.57e-13	42
smooth muscle myoblast	2.57e-13	42
muscle cell	5.89e-13	54
muscle precursor cell	1.32e-12	57
myoblast	1.32e-12	57
multi-potent skeletal muscle stem cell	1.32e-12	57
multi fate stem cell	2.86e-12	430
somatic stem cell	7.51e-12	436
stem cell	1.96e-11	444
lining cell	1.27e-10	57
barrier cell	1.27e-10	57
vascular associated smooth muscle cell	2.38e-10	32
myeloid cell	1.27e-09	112
common myeloid progenitor	1.27e-09	112
electrically responsive cell	2.08e-09	60
electrically active cell	2.08e-09	60
meso-epithelial cell	2.74e-09	44
endothelial cell	5.70e-09	35
columnar/cuboidal epithelial cell	1.71e-07	27
epithelial cell	2.45e-07	254

Uber Anatomy

Ontology term	p-value	n
lateral plate mesoderm	5.42e-34	216
musculoskeletal system	2.83e-30	167
mesoderm	7.34e-27	448
mesoderm-derived structure	7.34e-27	448
presumptive mesoderm	7.34e-27	448
bone marrow	7.66e-21	80
bone element	3.76e-19	86
skeletal element	3.82e-19	101
skeletal system	3.82e-19	101
immune system	1.69e-18	115
epithelial tube	1.07e-15	118
vasculature	3.74e-15	79
vascular system	3.74e-15	79
trunk mesenchyme	5.26e-15	143
hemolymphoid system	9.38e-15	112
anatomical system	9.66e-15	625
anatomical group	2.26e-14	626
hematopoietic system	6.11e-14	102
blood island	6.11e-14	102
cardiovascular system	7.25e-14	110
splanchnic layer of lateral plate mesoderm	1.04e-13	84
somite	6.10e-13	83
paraxial mesoderm	6.10e-13	83
presomitic mesoderm	6.10e-13	83
presumptive segmental plate	6.10e-13	83
trunk paraxial mesoderm	6.10e-13	83
presumptive paraxial mesoderm	6.10e-13	83
vessel	7.91e-13	69
circulatory system	8.03e-13	113
multi-cellular organism	1.94e-12	659
germ layer	2.30e-12	604
embryonic tissue	2.30e-12	604
presumptive structure	2.30e-12	604
epiblast (generic)	2.30e-12	604
embryonic structure	2.54e-12	605
developing anatomical structure	2.54e-12	605
blood vessel	2.63e-12	60
epithelial tube open at both ends	2.63e-12	60
blood vasculature	2.63e-12	60
vascular cord	2.63e-12	60
dermomyotome	4.08e-12	70
multilaminar epithelium	5.59e-12	82
unilaminar epithelium	6.07e-12	138
artery	1.65e-11	42
arterial blood vessel	1.65e-11	42
arterial system	1.65e-11	42
embryo	2.82e-11	612
skeletal muscle tissue	1.02e-10	61
striated muscle tissue	1.02e-10	61
myotome	1.02e-10	61
muscle tissue	4.12e-10	63
musculature	4.12e-10	63
musculature of body	4.12e-10	63
trunk	3.08e-08	216
systemic artery	3.38e-08	33
systemic arterial system	3.38e-08	33

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
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

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This analysis result is provided for C0 - C305 clusters.