Coexpression cluster:C247

Full id: C247_pons_locus_medulla_spinal_paracentral_medial_occipital

Phase1 CAGE Peaks

Hg19::chr10:105037601..105037624,+	p4@INA
Hg19::chr10:105037641..105037652,+	p16@INA
Hg19::chr10:121578268..121578279,+	p6@INPP5F
Hg19::chr10:79938937..79938973,+	p@chr10:79938937..79938973 +
Hg19::chr10:88718397..88718424,+	p3@SNCG
Hg19::chr12:107974646..107974657,+	p6@BTBD11
Hg19::chr12:5019095..5019105,+	p3@ENST00000542043
Hg19::chr12:5019108..5019119,+	p1@ENST00000542043
Hg19::chr12:6579808..6579815,-	p2@VAMP1
Hg19::chr12:6579833..6579850,-	p1@VAMP1
Hg19::chr13:25946216..25946235,+	p5@ATP8A2
Hg19::chr13:29646198..29646211,+	p5@MTUS2
Hg19::chr15:43803143..43803158,+	p2@MAP1A
Hg19::chr15:83378526..83378537,-	p7@AP3B2
Hg19::chr16:29909708..29909739,-	p@chr16:29909708..29909739 -
Hg19::chr16:31021916..31021920,-	p3@STX1B
Hg19::chr16:67189374..67189388,-	p@chr16:67189374..67189388 -
Hg19::chr17:7115127..7115145,-	p@chr17:7115127..7115145 -
Hg19::chr18:5577640..5577652,-	p14@EPB41L3
Hg19::chr18:5577655..5577670,-	p17@EPB41L3
Hg19::chr18:70209396..70209407,-	p@chr18:70209396..70209407 -
Hg19::chr1:202679535..202679553,-	p2@SYT2
Hg19::chr1:202679556..202679619,-	p1@SYT2
Hg19::chr1:202679624..202679645,-	p3@SYT2
Hg19::chr1:7788387..7788404,+	p@chr1:7788387..7788404 +
Hg19::chr21:31312275..31312287,-	p3@GRIK1
Hg19::chr21:31312328..31312347,-	p2@GRIK1
Hg19::chr21:31312348..31312362,-	p4@GRIK1
Hg19::chr21:34100341..34100356,-	p5@SYNJ1
Hg19::chr21:47851604..47851613,+	p@chr21:47851604..47851613 +
Hg19::chr22:29876197..29876215,+	p1@NEFH
Hg19::chr22:29886248..29886264,+	p@chr22:29886248..29886264 +
Hg19::chr22:36635684..36635733,-	p3@APOL2
Hg19::chr2:167005607..167005628,-	p2@SCN1A
Hg19::chr2:196440724..196440739,+	p15@SLC39A10
Hg19::chr2:218873244..218873256,-	p@chr2:218873244..218873256 -
Hg19::chr3:10857905..10857920,+	p1@SLC6A11
Hg19::chr3:56809534..56809564,-	p9@ARHGEF3
Hg19::chr3:9745487..9745502,+	p2@CPNE9
Hg19::chr4:9783252..9783264,+	p1@DRD5
Hg19::chr5:142065223..142065256,-	p6@FGF1
Hg19::chr5:161494723..161494732,+	p15@GABRG2
Hg19::chr6:143929375..143929393,+	p5@PHACTR2
Hg19::chr6:46293320..46293331,-	p7@RCAN2
Hg19::chr6:72926685..72926703,+	p18@RIMS1
Hg19::chr7:100493699..100493740,-	p3@ACHE
Hg19::chr7:100493744..100493759,-	p4@ACHE
Hg19::chr7:126892303..126892311,-	p4@GRM8
Hg19::chr7:31092185..31092196,+	p8@ADCYAP1R1
Hg19::chr7:38671067..38671081,-	p4@AMPH
Hg19::chr7:752742..752786,-	p5@PRKAR1B
Hg19::chr8:24771265..24771282,+	p1@NEFM
Hg19::chr8:24814118..24814133,-	p1@NEFL

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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p.value	FDR	nGenes	nPathway	Name
1.68021345890663e-05	0.00265893779871974	5	272	Neuroactive ligand-receptor interaction (KEGG):04080
3.47189991265201e-05	0.00439542528941744	3	53	Amyotrophic lateral sclerosis (ALS) (KEGG):05014
0.0001061436277718	0.0111981527299249	5	401	Transmembrane transport of small molecules (Reactome):REACT_15518
1.1460283977764e-07	7.25435975792461e-05	6	197	Synaptic Transmission (Reactome):REACT_13685
1.24432917686229e-06	0.000262553456317944	3	18	Botulinum neurotoxicity (Reactome):REACT_11184
8.907224977488e-07	0.000262553456317944	4	62	{VAMP2,63} (Static Module):NA

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:0060053	neurofilament cytoskeleton	5.76452463698256e-09
GO:0005883	neurofilament	5.76452463698256e-09
GO:0044459	plasma membrane part	5.39356905720145e-07
GO:0030054	cell junction	5.39356905720145e-07
GO:0007268	synaptic transmission	6.66485268915385e-07
GO:0060052	neurofilament cytoskeleton organization and biogenesis	6.66485268915385e-07
GO:0051234	establishment of localization	1.10714024149718e-06
GO:0019226	transmission of nerve impulse	1.19931140373097e-06
GO:0051179	localization	2.90696985444759e-06
GO:0006810	transport	4.32552140686666e-06
GO:0007267	cell-cell signaling	4.32552140686666e-06
GO:0045104	intermediate filament cytoskeleton organization and biogenesis	1.20627154453211e-05
GO:0045103	intermediate filament-based process	1.39099149236477e-05
GO:0045110	intermediate filament bundle assembly	3.35002810673953e-05
GO:0005887	integral to plasma membrane	6.93337190746111e-05
GO:0005886	plasma membrane	6.93337190746111e-05
GO:0032501	multicellular organismal process	6.93337190746111e-05
GO:0031226	intrinsic to plasma membrane	6.93337190746111e-05
GO:0030424	axon	0.000123706784522979
GO:0045109	intermediate filament organization	0.0002341018288924
GO:0030135	coated vesicle	0.000267933225744423
GO:0016192	vesicle-mediated transport	0.000418809417604697
GO:0008088	axon cargo transport	0.000568172251123635
GO:0007275	multicellular organismal development	0.000568172251123635
GO:0005856	cytoskeleton	0.000698920488850127
GO:0007399	nervous system development	0.000902372266977661
GO:0008021	synaptic vesicle	0.000920014325211797
GO:0006836	neurotransmitter transport	0.00102372330387087
GO:0044425	membrane part	0.00102372330387087
GO:0043005	neuron projection	0.00108511220980445
GO:0005882	intermediate filament	0.00112117144533564
GO:0045111	intermediate filament cytoskeleton	0.00112117144533564
GO:0005200	structural constituent of cytoskeleton	0.0011391566271197
GO:0050804	regulation of synaptic transmission	0.00164217168261946
GO:0050877	neurological system process	0.00192181601951179
GO:0051969	regulation of transmission of nerve impulse	0.00192181601951179
GO:0048489	synaptic vesicle transport	0.00192181601951179
GO:0016044	membrane organization and biogenesis	0.00192883952669166
GO:0007270	nerve-nerve synaptic transmission	0.00203660384954451
GO:0022892	substrate-specific transporter activity	0.00205606845313884
GO:0015075	ion transmembrane transporter activity	0.00214531373740093
GO:0044430	cytoskeletal part	0.00214531373740093
GO:0030136	clathrin-coated vesicle	0.00214531373740093
GO:0042995	cell projection	0.00241759306773508
GO:0005230	extracellular ligand-gated ion channel activity	0.00301010924667021
GO:0031644	regulation of neurological process	0.00301895377699923
GO:0016023	cytoplasmic membrane-bound vesicle	0.00335209651229851
GO:0031988	membrane-bound vesicle	0.00346540054964109
GO:0007154	cell communication	0.00365036465590875
GO:0042165	neurotransmitter binding	0.00365036465590875
GO:0048856	anatomical structure development	0.00384311493099898
GO:0022891	substrate-specific transmembrane transporter activity	0.0040609291840681
GO:0003008	system process	0.00427800408195558
GO:0051649	establishment of cellular localization	0.00446159307994661
GO:0044456	synapse part	0.00450748968317031
GO:0022834	ligand-gated channel activity	0.0045637709753216
GO:0015276	ligand-gated ion channel activity	0.0045637709753216
GO:0016043	cellular component organization and biogenesis	0.0045637709753216
GO:0051641	cellular localization	0.00466686851699799
GO:0048731	system development	0.00486533136937667
GO:0032502	developmental process	0.00514003969057503
GO:0022857	transmembrane transporter activity	0.00526040200093909
GO:0031410	cytoplasmic vesicle	0.00531710148004648
GO:0005234	extracellular-glutamate-gated ion channel activity	0.00531710148004648
GO:0031982	vesicle	0.00553543088521537
GO:0045761	regulation of adenylate cyclase activity	0.00569918910307809
GO:0051339	regulation of lyase activity	0.00580484496877022
GO:0031279	regulation of cyclase activity	0.00580484496877022
GO:0005515	protein binding	0.00627792290736801
GO:0010324	membrane invagination	0.00627792290736801
GO:0006897	endocytosis	0.00627792290736801
GO:0060181	female receptivity	0.00655659780821679
GO:0045924	regulation of female receptivity	0.00655659780821679
GO:0033596	TSC1-TSC2 complex	0.00655659780821679
GO:0060180	female mating behavior	0.00655659780821679
GO:0050795	regulation of behavior	0.00655659780821679
GO:0032222	regulation of synaptic transmission, cholinergic	0.00655659780821679
GO:0032223	negative regulation of synaptic transmission, cholinergic	0.00655659780821679
GO:0008090	retrograde axon cargo transport	0.00655659780821679
GO:0001589	dopamine D5 receptor activity	0.00655659780821679
GO:0033693	neurofilament bundle assembly	0.00655659780821679
GO:0022836	gated channel activity	0.00783831692333591
GO:0046907	intracellular transport	0.00911087086016492
GO:0001507	acetylcholine catabolic process in synaptic cleft	0.0110593733437102
GO:0043237	laminin-1 binding	0.0110593733437102
GO:0003990	acetylcholinesterase activity	0.0110593733437102
GO:0033057	reproductive behavior in a multicellular organism	0.0110593733437102
GO:0019896	axon transport of mitochondrion	0.0110593733437102
GO:0031133	regulation of axon diameter	0.0110593733437102
GO:0050805	negative regulation of synaptic transmission	0.0110593733437102
GO:0006581	acetylcholine catabolic process	0.0110593733437102
GO:0001994	norepinephrine-epinephrine vasoconstriction involved in regulation of systemic arterial blood pressure	0.0110593733437102
GO:0030818	negative regulation of cAMP biosynthetic process	0.0110593733437102
GO:0030815	negative regulation of cAMP metabolic process	0.0110593733437102
GO:0051966	regulation of synaptic transmission, glutamatergic	0.0110593733437102
GO:0001588	dopamine D1 receptor-like receptor activity	0.0110593733437102
GO:0019932	second-messenger-mediated signaling	0.0111195460700301
GO:0005231	excitatory extracellular ligand-gated ion channel activity	0.0117553069406724
GO:0001505	regulation of neurotransmitter levels	0.0136251482154584
GO:0032940	secretion by cell	0.0142129165712312
GO:0016020	membrane	0.0142129165712312
GO:0007188	G-protein signaling, coupled to cAMP nucleotide second messenger	0.0142129165712312
GO:0043236	laminin binding	0.0142129165712312
GO:0008291	acetylcholine metabolic process	0.0142129165712312
GO:0030800	negative regulation of cyclic nucleotide metabolic process	0.0142129165712312
GO:0030346	protein phosphatase 2B binding	0.0142129165712312
GO:0030809	negative regulation of nucleotide biosynthetic process	0.0142129165712312
GO:0001992	regulation of systemic arterial blood pressure by vasopressin	0.0142129165712312
GO:0030803	negative regulation of cyclic nucleotide biosynthetic process	0.0142129165712312
GO:0051970	negative regulation of transmission of nerve impulse	0.0142129165712312
GO:0042220	response to cocaine	0.0142129165712312
GO:0014073	response to tropane	0.0142129165712312
GO:0019933	cAMP-mediated signaling	0.0147949686011322
GO:0005216	ion channel activity	0.0167255681365211
GO:0008066	glutamate receptor activity	0.0168727651275069
GO:0007010	cytoskeleton organization and biogenesis	0.0168727651275069
GO:0022838	substrate specific channel activity	0.0169913913045988
GO:0022803	passive transmembrane transporter activity	0.0171090747376351
GO:0015267	channel activity	0.0171090747376351
GO:0004104	cholinesterase activity	0.0171090747376351
GO:0035249	synaptic transmission, glutamatergic	0.0171090747376351
GO:0007191	dopamine receptor, adenylate cyclase activating pathway	0.0171090747376351
GO:0002076	osteoblast development	0.0171090747376351
GO:0050840	extracellular matrix binding	0.0171090747376351
GO:0043228	non-membrane-bound organelle	0.0177843020348907
GO:0043232	intracellular non-membrane-bound organelle	0.0177843020348907
GO:0008306	associative learning	0.0199303464299923
GO:0008035	high-density lipoprotein binding	0.0199303464299923
GO:0030817	regulation of cAMP biosynthetic process	0.0199303464299923
GO:0008089	anterograde axon cargo transport	0.0199303464299923
GO:0001993	regulation of systemic arterial blood pressure by norepinephrine-epinephrine	0.0199303464299923
GO:0004439	phosphoinositide 5-phosphatase activity	0.0199303464299923
GO:0042439	ethanolamine and derivative metabolic process	0.0199303464299923
GO:0046903	secretion	0.0220853584299826
GO:0007187	G-protein signaling, coupled to cyclic nucleotide second messenger	0.0220853584299826
GO:0031594	neuromuscular junction	0.0222341222275618
GO:0019098	reproductive behavior	0.0222341222275618
GO:0030802	regulation of cyclic nucleotide biosynthetic process	0.0222341222275618
GO:0030808	regulation of nucleotide biosynthetic process	0.0222341222275618
GO:0007617	mating behavior	0.0222341222275618
GO:0045980	negative regulation of nucleotide metabolic process	0.0222341222275618
GO:0048488	synaptic vesicle endocytosis	0.0222341222275618
GO:0030814	regulation of cAMP metabolic process	0.0222341222275618
GO:0019935	cyclic-nucleotide-mediated signaling	0.0224568120805291
GO:0022607	cellular component assembly	0.0245546746794124
GO:0031645	negative regulation of neurological process	0.0245546746794124
GO:0003084	positive regulation of systemic arterial blood pressure	0.0245546746794124
GO:0005332	gamma-aminobutyric acid:sodium symporter activity	0.0245546746794124
GO:0001963	synaptic transmission, dopaminergic	0.0245546746794124
GO:0030799	regulation of cyclic nucleotide metabolic process	0.0245546746794124
GO:0008503	benzodiazepine receptor activity	0.0245546746794124
GO:0009611	response to wounding	0.0254724008806108
GO:0006869	lipid transport	0.0257109825227417
GO:0004445	inositol-polyphosphate 5-phosphatase activity	0.0259850654483273
GO:0045776	negative regulation of blood pressure	0.0259850654483273
GO:0042135	neurotransmitter catabolic process	0.0259850654483273
GO:0050886	endocrine process	0.0259850654483273
GO:0001990	regulation of systemic arterial blood pressure by hormone	0.0259850654483273
GO:0015185	L-gamma-aminobutyric acid transmembrane transporter activity	0.0259850654483273
GO:0016079	synaptic vesicle exocytosis	0.0259850654483273
GO:0043279	response to alkaloid	0.0259850654483273
GO:0015277	kainate selective glutamate receptor activity	0.0259850654483273
GO:0046030	inositol trisphosphate phosphatase activity	0.0259850654483273
GO:0030594	neurotransmitter receptor activity	0.0260856382739532
GO:0045211	postsynaptic membrane	0.0286922244060811
GO:0031526	brush border membrane	0.0286922244060811
GO:0001540	beta-amyloid binding	0.0313005149388685
GO:0006140	regulation of nucleotide metabolic process	0.0313005149388685
GO:0045777	positive regulation of blood pressure	0.0313005149388685
GO:0045184	establishment of protein localization	0.0324215379354728
GO:0042402	biogenic amine catabolic process	0.033619649627795
GO:0014070	response to organic cyclic substance	0.033619649627795
GO:0031253	cell projection membrane	0.033619649627795
GO:0046873	metal ion transmembrane transporter activity	0.0348795867831052
GO:0042577	lipid phosphatase activity	0.0348795867831052
GO:0003044	regulation of systemic arterial blood pressure mediated by a chemical signal	0.0348795867831052
GO:0051705	behavioral interaction between organisms	0.0348795867831052
GO:0007271	synaptic transmission, cholinergic	0.0348795867831052
GO:0042734	presynaptic membrane	0.0348795867831052
GO:0005283	sodium:amino acid symporter activity	0.0348795867831052
GO:0007618	mating	0.0348795867831052
GO:0008104	protein localization	0.0348795867831052
GO:0007018	microtubule-based movement	0.0367252912294252
GO:0005416	cation:amino acid symporter activity	0.0367252912294252
GO:0030866	cortical actin cytoskeleton organization and biogenesis	0.0367252912294252
GO:0004999	vasoactive intestinal polypeptide receptor activity	0.0367252912294252
GO:0017156	calcium ion-dependent exocytosis	0.0367252912294252
GO:0006886	intracellular protein transport	0.0378025738124215
GO:0030865	cortical cytoskeleton organization and biogenesis	0.0383055765245929
GO:0042982	amyloid precursor protein metabolic process	0.0383055765245929
GO:0030552	cAMP binding	0.0383055765245929
GO:0042219	amino acid derivative catabolic process	0.0383055765245929
GO:0044464	cell part	0.0383055765245929
GO:0033036	macromolecule localization	0.0389750845834086
GO:0007194	negative regulation of adenylate cyclase activity	0.0401888459378791
GO:0051350	negative regulation of lyase activity	0.0401888459378791
GO:0031280	negative regulation of cyclase activity	0.0401888459378791
GO:0030705	cytoskeleton-dependent intracellular transport	0.0405545026518932
GO:0003073	regulation of systemic arterial blood pressure	0.0419964870842404
GO:0042310	vasoconstriction	0.0419964870842404
GO:0050714	positive regulation of protein secretion	0.0419964870842404
GO:0016021	integral to membrane	0.0432250967315281
GO:0030137	COPI-coated vesicle	0.0433088025382806
GO:0050435	beta-amyloid metabolic process	0.0433088025382806
GO:0007212	dopamine receptor signaling pathway	0.0433088025382806
GO:0019903	protein phosphatase binding	0.0433088025382806
GO:0007612	learning	0.0433088025382806
GO:0008289	lipid binding	0.0434730328223996
GO:0031224	intrinsic to membrane	0.0438426697017679
GO:0001518	voltage-gated sodium channel complex	0.0451813700461926
GO:0004012	phospholipid-translocating ATPase activity	0.0463462548699017
GO:0006171	cAMP biosynthetic process	0.0463462548699017
GO:0015247	aminophospholipid transporter activity	0.0463462548699017
GO:0035240	dopamine binding	0.0463462548699017
GO:0004952	dopamine receptor activity	0.0463462548699017
GO:0005518	collagen binding	0.0463462548699017
GO:0007601	visual perception	0.0469904287170701
GO:0050953	sensory perception of light stimulus	0.0469904287170701
GO:0006892	post-Golgi vesicle-mediated transport	0.0497964531035081
GO:0007215	glutamate signaling pathway	0.0497964531035081
GO:0051047	positive regulation of secretion	0.0497964531035081
GO:0016208	AMP binding	0.0497964531035081

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><br>uberon_data<br><br>

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Uber Anatomy

Ontology term	p-value	n
central nervous system	1.05e-39	82
regional part of nervous system	4.89e-35	94
nervous system	4.89e-35	94
neural tube	2.15e-33	57
neural rod	2.15e-33	57
future spinal cord	2.15e-33	57
neural keel	2.15e-33	57
brain	9.18e-33	69
future brain	9.18e-33	69
regional part of brain	3.01e-31	59
adult organism	3.50e-31	115
ectoderm	3.44e-26	173
presumptive ectoderm	3.44e-26	173
ectoderm-derived structure	1.56e-25	169
anterior neural tube	5.41e-25	42
regional part of forebrain	7.48e-25	41
forebrain	7.48e-25	41
future forebrain	7.48e-25	41
neurectoderm	6.65e-24	90
neural plate	2.02e-23	86
presumptive neural plate	2.02e-23	86
anterior region of body	4.73e-23	129
craniocervical region	4.73e-23	129
head	5.54e-22	123
gray matter	6.82e-21	34
brain grey matter	6.82e-21	34
telencephalon	7.98e-21	34
regional part of telencephalon	3.92e-20	33
cerebral hemisphere	1.04e-19	32
pre-chordal neural plate	1.61e-16	61
regional part of cerebral cortex	1.50e-15	22
cerebral cortex	1.75e-15	25
pallium	1.75e-15	25
neocortex	2.25e-14	20
posterior neural tube	1.94e-09	15
chordal neural plate	1.94e-09	15
organism subdivision	4.27e-09	365
segmental subdivision of nervous system	3.81e-08	13
segmental subdivision of hindbrain	1.27e-07	12
hindbrain	1.27e-07	12
presumptive hindbrain	1.27e-07	12
nucleus of brain	7.07e-07	9
neural nucleus	7.07e-07	9
basal ganglion	9.78e-07	9
nuclear complex of neuraxis	9.78e-07	9
aggregate regional part of brain	9.78e-07	9
collection of basal ganglia	9.78e-07	9
cerebral subcortex	9.78e-07	9

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
MAFK#7975	8	4.0906767000498	0.000688049742804444	0.005548118212535
SUZ12#23512	5	4.72790385953424	0.00409161190914499	0.0195365910565169

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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