Coexpression cluster:C1986

Full id: C1986_Preadipocyte_Mesenchymal_basal_Fibroblast_Ewing_hepatic_Adipocyte

Phase1 CAGE Peaks

Hg19::chr7:134464377..134464413,+	p1@CALD1
Hg19::chr7:134464414..134464425,+	p6@CALD1
Hg19::chr7:134464465..134464476,+	p7@CALD1
Hg19::chr7:134655216..134655252,+	p42@CALD1
Hg19::chr7:41740181..41740234,-	p3@INHBA

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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GO ID	GO name	FDR corrected p-value
GO:0048180	activin complex	0.00274327425429597
GO:0043509	activin A complex	0.00274327425429597
GO:0043511	inhibin complex	0.00274327425429597
GO:0043512	inhibin A complex	0.00274327425429597
GO:0045077	negative regulation of interferon-gamma biosynthetic process	0.00274327425429597
GO:0045650	negative regulation of macrophage differentiation	0.00274327425429597
GO:0032278	positive regulation of gonadotropin secretion	0.00274327425429597
GO:0046881	positive regulation of follicle-stimulating hormone secretion	0.00274327425429597
GO:0045578	negative regulation of B cell differentiation	0.00274327425429597
GO:0032276	regulation of gonadotropin secretion	0.00274327425429597
GO:0046880	regulation of follicle-stimulating hormone secretion	0.00274327425429597
GO:0046887	positive regulation of hormone secretion	0.00274327425429597
GO:0048184	follistatin binding	0.00274327425429597
GO:0046882	negative regulation of follicle-stimulating hormone secretion	0.00274327425429597
GO:0042541	hemoglobin biosynthetic process	0.00274327425429597
GO:0045620	negative regulation of lymphocyte differentiation	0.00274327425429597
GO:0032277	negative regulation of gonadotropin secretion	0.00274327425429597
GO:0017106	activin inhibitor activity	0.00274327425429597
GO:0032925	regulation of activin receptor signaling pathway	0.00274327425429597
GO:0045649	regulation of macrophage differentiation	0.00274327425429597
GO:0032274	gonadotropin secretion	0.00274327425429597
GO:0020027	hemoglobin metabolic process	0.00274327425429597
GO:0032924	activin receptor signaling pathway	0.00274327425429597
GO:0046884	follicle-stimulating hormone secretion	0.00274327425429597
GO:0045648	positive regulation of erythrocyte differentiation	0.00274327425429597
GO:0050869	negative regulation of B cell activation	0.00316526985601304
GO:0045577	regulation of B cell differentiation	0.0039187901672028
GO:0017022	myosin binding	0.0039187901672028
GO:0002762	negative regulation of myeloid leukocyte differentiation	0.00425655424855442
GO:0030225	macrophage differentiation	0.00457171996631325
GO:0005160	transforming growth factor beta receptor binding	0.00457171996631325
GO:0046888	negative regulation of hormone secretion	0.00457171996631325
GO:0045646	regulation of erythrocyte differentiation	0.00457171996631325
GO:0045072	regulation of interferon-gamma biosynthetic process	0.00469189024750552
GO:0042326	negative regulation of phosphorylation	0.00469189024750552
GO:0045639	positive regulation of myeloid cell differentiation	0.00469189024750552
GO:0042095	interferon-gamma biosynthetic process	0.00469189024750552
GO:0045936	negative regulation of phosphate metabolic process	0.00469189024750552
GO:0002761	regulation of myeloid leukocyte differentiation	0.00527475089124858
GO:0045619	regulation of lymphocyte differentiation	0.00535186357924799
GO:0042036	negative regulation of cytokine biosynthetic process	0.00535186357924799
GO:0051048	negative regulation of secretion	0.00548549865239052
GO:0001541	ovarian follicle development	0.00548549865239052
GO:0032609	interferon-gamma production	0.00548549865239052
GO:0045638	negative regulation of myeloid cell differentiation	0.00548549865239052
GO:0046883	regulation of hormone secretion	0.00554377340373417
GO:0051250	negative regulation of lymphocyte activation	0.00554377340373417
GO:0051047	positive regulation of secretion	0.00587706040487411
GO:0005523	tropomyosin binding	0.00587706040487411
GO:0022601	menstrual cycle phase	0.00658201692404939
GO:0022602	menstrual cycle process	0.00659246796298695
GO:0050864	regulation of B cell activation	0.00659246796298695
GO:0008585	female gonad development	0.0069853226122356
GO:0030183	B cell differentiation	0.00710061156532613
GO:0046545	development of primary female sexual characteristics	0.00710061156532613
GO:0046660	female sex differentiation	0.00710061156532613
GO:0002573	myeloid leukocyte differentiation	0.0072164862557348
GO:0030218	erythrocyte differentiation	0.00751867023133696
GO:0042698	menstrual cycle	0.00751867023133696
GO:0045637	regulation of myeloid cell differentiation	0.00751867023133696
GO:0000082	G1/S transition of mitotic cell cycle	0.00751867023133696
GO:0046879	hormone secretion	0.00751867023133696
GO:0017148	negative regulation of translation	0.00892179721406047
GO:0031327	negative regulation of cellular biosynthetic process	0.00963864524147757
GO:0045597	positive regulation of cell differentiation	0.00991186012605939
GO:0009890	negative regulation of biosynthetic process	0.0104817334367983
GO:0008406	gonad development	0.0104817334367983
GO:0048608	reproductive structure development	0.0104817334367983
GO:0030308	negative regulation of cell growth	0.0105283196439338
GO:0045792	negative regulation of cell size	0.010573569048139
GO:0051046	regulation of secretion	0.0108572593869365
GO:0045137	development of primary sexual characteristics	0.0108572593869365
GO:0042035	regulation of cytokine biosynthetic process	0.0108572593869365
GO:0048609	reproductive process in a multicellular organism	0.0108572593869365
GO:0032504	multicellular organism reproduction	0.0108572593869365
GO:0042113	B cell activation	0.0108572593869365
GO:0045926	negative regulation of growth	0.0108572593869365
GO:0042325	regulation of phosphorylation	0.0111023468893183
GO:0030098	lymphocyte differentiation	0.0111023468893183
GO:0045596	negative regulation of cell differentiation	0.0111239770299129
GO:0042089	cytokine biosynthetic process	0.0111239770299129
GO:0042107	cytokine metabolic process	0.0111239770299129
GO:0051094	positive regulation of developmental process	0.0111239770299129
GO:0051174	regulation of phosphorus metabolic process	0.0111239770299129
GO:0019220	regulation of phosphate metabolic process	0.0111239770299129
GO:0003001	generation of a signal involved in cell-cell signaling	0.0111538065677599
GO:0007178	transmembrane receptor protein serine/threonine kinase signaling pathway	0.0117226808852989
GO:0051249	regulation of lymphocyte activation	0.0117226808852989
GO:0030099	myeloid cell differentiation	0.0117226808852989
GO:0051093	negative regulation of developmental process	0.0117226808852989
GO:0050865	regulation of cell activation	0.0120450365843769
GO:0007548	sex differentiation	0.0120628609213449
GO:0051329	interphase of mitotic cell cycle	0.012521706120398
GO:0003006	reproductive developmental process	0.0126796167943465
GO:0002521	leukocyte differentiation	0.0128430095254642
GO:0051325	interphase	0.0128430095254642
GO:0007050	cell cycle arrest	0.0142618136123162
GO:0051248	negative regulation of protein metabolic process	0.0145349377240317
GO:0001816	cytokine production	0.0156311719386937
GO:0045944	positive regulation of transcription from RNA polymerase II promoter	0.019028151025804
GO:0005516	calmodulin binding	0.0191102653726784
GO:0045595	regulation of cell differentiation	0.019324669846072
GO:0046649	lymphocyte activation	0.0205955677522962
GO:0030097	hemopoiesis	0.0211016001926894
GO:0001558	regulation of cell growth	0.0211016001926894
GO:0003012	muscle system process	0.0211016001926894
GO:0006936	muscle contraction	0.0211016001926894
GO:0048534	hemopoietic or lymphoid organ development	0.0219172624202018
GO:0045321	leukocyte activation	0.0225925424131273
GO:0002520	immune system development	0.0226352337476506
GO:0006417	regulation of translation	0.0226771413179177
GO:0031326	regulation of cellular biosynthetic process	0.0241143574865719
GO:0016049	cell growth	0.0241143574865719
GO:0040008	regulation of growth	0.0241143574865719
GO:0008361	regulation of cell size	0.0243210210561916
GO:0001501	skeletal development	0.0243210210561916
GO:0001775	cell activation	0.0243210210561916
GO:0006917	induction of apoptosis	0.0243210210561916
GO:0012502	induction of programmed cell death	0.0243210210561916
GO:0032501	multicellular organismal process	0.0243210210561916
GO:0005179	hormone activity	0.0243210210561916
GO:0009889	regulation of biosynthetic process	0.0243210210561916
GO:0045893	positive regulation of transcription, DNA-dependent	0.0247880963368237
GO:0045786	negative regulation of progression through cell cycle	0.0248079815534451
GO:0050793	regulation of developmental process	0.0258084567133596
GO:0008083	growth factor activity	0.0274410651209666
GO:0043065	positive regulation of apoptosis	0.0275441036420166
GO:0043068	positive regulation of programmed cell death	0.0275441036420166
GO:0051239	regulation of multicellular organismal process	0.0293187191323811
GO:0045941	positive regulation of transcription	0.0293187191323811
GO:0045935	positive regulation of nucleobase, nucleoside, nucleotide and nucleic acid metabolic process	0.0301332864785564
GO:0051179	localization	0.0307047454263562
GO:0007167	enzyme linked receptor protein signaling pathway	0.0308048393720118
GO:0022414	reproductive process	0.0310822373624248
GO:0005125	cytokine activity	0.0313554509768971
GO:0000278	mitotic cell cycle	0.0327235991619901
GO:0000074	regulation of progression through cell cycle	0.0351611490324562
GO:0051726	regulation of cell cycle	0.0354965159760112
GO:0042802	identical protein binding	0.0355710461104435
GO:0031325	positive regulation of cellular metabolic process	0.0355710461104435
GO:0022403	cell cycle phase	0.0357037107339966
GO:0031324	negative regulation of cellular metabolic process	0.036122093213212
GO:0006928	cell motility	0.036122093213212
GO:0051674	localization of cell	0.036122093213212
GO:0046903	secretion	0.036122093213212
GO:0009893	positive regulation of metabolic process	0.0365248623183854
GO:0051246	regulation of protein metabolic process	0.0389616696652158
GO:0006357	regulation of transcription from RNA polymerase II promoter	0.0389616696652158
GO:0009892	negative regulation of metabolic process	0.0397965356152556
GO:0003779	actin binding	0.0397965356152556
GO:0000902	cell morphogenesis	0.0428340666047415
GO:0032989	cellular structure morphogenesis	0.0428340666047415
GO:0005615	extracellular space	0.0469705347814123

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	2.34e-32	180
fibroblast	2.98e-16	75
mesodermal cell	5.23e-12	119
muscle precursor cell	9.96e-12	57
myoblast	9.96e-12	57
multi-potent skeletal muscle stem cell	9.96e-12	57
electrically responsive cell	1.70e-11	60
electrically active cell	1.70e-11	60
muscle cell	2.41e-11	54
embryonic cell	2.50e-11	248
smooth muscle cell	3.02e-10	42
smooth muscle myoblast	3.02e-10	42
contractile cell	5.08e-10	59
vascular associated smooth muscle cell	1.11e-09	32
skin fibroblast	1.75e-07	23
preadipocyte	6.95e-07	12

Uber Anatomy

Ontology term	p-value	n
multi-cellular organism	5.51e-19	659
organism subdivision	8.31e-15	365
anatomical system	1.20e-14	625
somite	1.29e-14	83
paraxial mesoderm	1.29e-14	83
presomitic mesoderm	1.29e-14	83
presumptive segmental plate	1.29e-14	83
trunk paraxial mesoderm	1.29e-14	83
presumptive paraxial mesoderm	1.29e-14	83
splanchnic layer of lateral plate mesoderm	1.47e-14	84
anatomical group	2.61e-14	626
vasculature	5.36e-14	79
vascular system	5.36e-14	79
muscle tissue	1.05e-12	63
musculature	1.05e-12	63
musculature of body	1.05e-12	63
trunk mesenchyme	1.68e-12	143
multilaminar epithelium	2.02e-12	82
dermomyotome	4.30e-12	70
skeletal muscle tissue	5.32e-12	61
striated muscle tissue	5.32e-12	61
myotome	5.32e-12	61
blood vessel	1.97e-11	60
epithelial tube open at both ends	1.97e-11	60
blood vasculature	1.97e-11	60
vascular cord	1.97e-11	60
vessel	4.38e-11	69
multi-tissue structure	4.60e-11	347
cardiovascular system	4.97e-11	110
circulatory system	1.11e-10	113
artery	3.24e-10	42
arterial blood vessel	3.24e-10	42
arterial system	3.24e-10	42
cell layer	4.83e-10	312
surface structure	5.58e-10	95
anatomical cluster	6.16e-10	286
epithelium	9.79e-10	309
trunk	1.36e-09	216
embryo	1.46e-09	612
epithelial tube	1.57e-09	118
unilaminar epithelium	2.04e-09	138
embryonic structure	3.13e-09	605
developing anatomical structure	3.13e-09	605
germ layer	5.55e-09	604
embryonic tissue	5.55e-09	604
presumptive structure	5.55e-09	604
epiblast (generic)	5.55e-09	604
systemic artery	9.53e-09	33
systemic arterial system	9.53e-09	33
anatomical conduit	9.72e-08	241
integument	1.55e-07	45
integumental system	1.55e-07	45
mesenchyme	2.64e-07	238
entire embryonic mesenchyme	2.64e-07	238
skin of body	7.39e-07	40

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
FOS#2353	3	5.39877318533664	0.0115389531727874	0.0421974414514776
FOXA1#3169	3	6.64885184963127	0.00638902516656872	0.0278107531101267
FOXA2#3170	3	14.7782782515991	0.000628919285119448	0.00517479722828252
GTF2F1#2962	3	7.64379652605459	0.0042841549641205	0.0203489567171994
JUN#3725	3	7.5076975154018	0.00451120655290603	0.0213390960269465
MXI1#4601	3	5.97694297725558	0.00865300488936688	0.0329569008293128
NR3C1#2908	3	8.98381399870382	0.00268799578894045	0.0147994934999817
RFX5#5993	3	7.22874649631706	0.0050291827895866	0.0234703436865648
SRF#6722	3	8.27830695730069	0.00340484607377615	0.0173640665608236
STAT3#6774	3	6.31167899829254	0.00741117212246054	0.0306164868991597
TAF7#6879	3	6.85984164295435	0.00584328640701904	0.0262525591096387
TRIM28#10155	3	11.1543150271575	0.00143315927152925	0.0092030079414193

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.