ISMARA results: Rfx3_Rfx1

Motif ID: Rfx3_Rfx1_Rfx4

Z-value: 2.661

Transcription factors associated with Rfx3_Rfx1_Rfx4:

Gene Symbol	Entrez ID	Gene Name
Rfx1	ENSMUSG00000031706.6	Rfx1
Rfx3	ENSMUSG00000040929.10	Rfx3
Rfx4	ENSMUSG00000020037.9	Rfx4

Activity-expression correlation:

Gene Symbol	Promoter	Pearson corr. coef.	P-value	Plot
Rfx1	mm10_v2_chr8_+_84066824_84066882	-0.32	4.1e-02	Click!
Rfx4	mm10_v2_chr10_+_84838143_84838153	-0.31	4.6e-02	Click!
Rfx3	mm10_v2_chr19_-_28010995_28011054	0.04	8.2e-01	Click!

Sorted Z-values for motif Rfx3_Rfx1_Rfx4

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Top targets:

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Promoter	Score	Refseq	Gene Symbol	Gene Name
chr18_+_60925612	32.716	ENSMUST00000102888.3 ENSMUST00000025519.4	Camk2a	calcium/calmodulin-dependent protein kinase II alpha
chr15_+_98167806	19.919	ENSMUST00000031914.4	AI836003	expressed sequence AI836003
chr7_-_31051431	18.797	ENSMUST00000073892.4	Fxyd7	FXYD domain-containing ion transport regulator 7
chr18_+_60925644	15.128	ENSMUST00000115297.1	Camk2a	calcium/calmodulin-dependent protein kinase II alpha
chr5_+_120431770	12.887	ENSMUST00000031591.7	Lhx5	LIM homeobox protein 5
chrX_+_7919816	12.788	ENSMUST00000041096.3	Pcsk1n	proprotein convertase subtilisin/kexin type 1 inhibitor
chr4_-_119415494	12.185	ENSMUST00000063642.2	Ccdc30	coiled-coil domain containing 30
chr5_+_24985840	10.671	ENSMUST00000075081.6	1500035N22Rik	RIKEN cDNA 1500035N22 gene
chr7_-_140082246	10.486	ENSMUST00000166758.2	Caly	calcyon neuron-specific vesicular protein
chr2_+_121289589	10.418	ENSMUST00000094639.3	Map1a	microtubule-associated protein 1 A
chr11_-_105944412	10.189	ENSMUST00000019734.4 ENSMUST00000184269.1 ENSMUST00000150563.1	Cyb561	cytochrome b-561
chr7_-_140082489	9.766	ENSMUST00000026541.7	Caly	calcyon neuron-specific vesicular protein
chr16_+_14906622	9.762	ENSMUST00000090277.1	Efcab1	EF hand calcium binding domain 1
chr7_+_99268338	9.348	ENSMUST00000107100.2	Map6	microtubule-associated protein 6
chr17_+_34629533	9.076	ENSMUST00000015620.6	Prrt1	proline-rich transmembrane protein 1
chr17_-_31277327	8.167	ENSMUST00000024832.7	Rsph1	radial spoke head 1 homolog (Chlamydomonas)
chr11_-_105944128	8.148	ENSMUST00000184086.1	Cyb561	cytochrome b-561
chr2_-_118256929	7.538	ENSMUST00000028820.6 ENSMUST00000028821.3	Fsip1	fibrous sheath-interacting protein 1
chr16_-_16829276	7.421	ENSMUST00000023468.5	Spag6	sperm associated antigen 6
chr11_-_6606053	7.144	ENSMUST00000045713.3	Nacad	NAC alpha domain containing

Gene Ontology Analysis

Gene overrepresentation in biological_process category:

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Showing 1 to 20 of 219 entries

Log-likelihood per target	Total log-likelihood	Term	Description
4.1	52.7	GO:0099628	receptor diffusion trapping(GO:0098953) postsynaptic neurotransmitter receptor diffusion trapping(GO:0098970) neurotransmitter receptor diffusion trapping(GO:0099628)
0.8	21.8	GO:0048268	clathrin coat assembly(GO:0048268)
0.2	18.7	GO:0022900	electron transport chain(GO:0022900)
0.3	15.4	GO:0007026	negative regulation of microtubule depolymerization(GO:0007026)
3.0	14.8	GO:2000325	regulation of ligand-dependent nuclear receptor transcription coactivator activity(GO:2000325) positive regulation of ligand-dependent nuclear receptor transcription coactivator activity(GO:2000327)
0.3	14.5	GO:2000649	regulation of sodium ion transmembrane transporter activity(GO:2000649)
0.6	13.0	GO:0045063	T-helper 1 cell differentiation(GO:0045063)
1.6	12.9	GO:0021937	cerebellar Purkinje cell-granule cell precursor cell signaling involved in regulation of granule cell precursor cell proliferation(GO:0021937)
0.7	12.8	GO:0016486	peptide hormone processing(GO:0016486)
1.4	12.5	GO:0048170	positive regulation of long-term neuronal synaptic plasticity(GO:0048170)
0.2	10.2	GO:0032418	lysosome localization(GO:0032418)
0.4	9.7	GO:0099517	anterograde synaptic vesicle transport(GO:0048490) synaptic vesicle cytoskeletal transport(GO:0099514) synaptic vesicle transport along microtubule(GO:0099517)
0.1	9.5	GO:0007286	spermatid development(GO:0007286)
0.4	9.2	GO:0071625	vocalization behavior(GO:0071625)
1.7	7.0	GO:0002924	negative regulation of humoral immune response mediated by circulating immunoglobulin(GO:0002924) negative regulation of interleukin-6 biosynthetic process(GO:0045409)
0.1	7.0	GO:0006626	protein targeting to mitochondrion(GO:0006626)
0.3	6.9	GO:0032011	ARF protein signal transduction(GO:0032011) regulation of ARF protein signal transduction(GO:0032012)
1.0	6.8	GO:0035093	spermatogenesis, exchange of chromosomal proteins(GO:0035093)
0.2	6.8	GO:0007189	adenylate cyclase-activating G-protein coupled receptor signaling pathway(GO:0007189)
0.3	6.3	GO:0060074	synapse maturation(GO:0060074)

Gene overrepresentation in cellular_component category:

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Showing 1 to 20 of 123 entries

Log-likelihood per target	Total log-likelihood	Term	Description
15.9	47.8	GO:0099573	glutamatergic postsynaptic density(GO:0099573)
0.0	30.6	GO:0005887	integral component of plasma membrane(GO:0005887)
0.1	23.8	GO:0098852	lysosomal membrane(GO:0005765) lytic vacuole membrane(GO:0098852)
0.1	19.1	GO:0016607	nuclear speck(GO:0016607)
0.1	17.5	GO:0005874	microtubule(GO:0005874)
0.1	13.7	GO:0030141	secretory granule(GO:0030141)
3.1	12.2	GO:1990769	proximal neuron projection(GO:1990769)
0.1	11.7	GO:0001669	acrosomal vesicle(GO:0001669)
1.2	9.3	GO:0001520	outer dense fiber(GO:0001520)
0.3	9.0	GO:0035371	microtubule plus-end(GO:0035371)
0.2	8.4	GO:0097546	ciliary base(GO:0097546)
0.5	8.2	GO:0005640	nuclear outer membrane(GO:0005640)
0.5	7.6	GO:1904115	axon cytoplasm(GO:1904115)
0.8	7.0	GO:0097442	CA3 pyramidal cell dendrite(GO:0097442)
0.1	7.0	GO:0097610	cleavage furrow(GO:0032154) cell surface furrow(GO:0097610)
0.2	6.8	GO:0097440	apical dendrite(GO:0097440)
0.0	6.7	GO:0005741	mitochondrial outer membrane(GO:0005741)
0.2	6.6	GO:0034451	centriolar satellite(GO:0034451)
0.2	6.5	GO:0035861	site of double-strand break(GO:0035861)
0.0	6.5	GO:0009986	cell surface(GO:0009986)

Gene overrepresentation in molecular_function category:

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Showing 1 to 20 of 150 entries

Log-likelihood per target	Total log-likelihood	Term	Description
4.1	49.5	GO:0009931	calcium-dependent protein serine/threonine kinase activity(GO:0009931)
0.1	37.2	GO:0008017	microtubule binding(GO:0008017)
2.5	20.3	GO:0032051	clathrin light chain binding(GO:0032051)
6.1	18.3	GO:0022865	transmembrane electron transfer carrier(GO:0022865)
0.4	15.2	GO:0017080	sodium channel regulator activity(GO:0017080)
0.5	14.8	GO:0032183	SUMO binding(GO:0032183)
0.3	12.2	GO:0004867	serine-type endopeptidase inhibitor activity(GO:0004867)
0.3	9.3	GO:0005112	Notch binding(GO:0005112)
0.9	7.2	GO:0004865	protein serine/threonine phosphatase inhibitor activity(GO:0004865)
0.9	7.0	GO:0005519	cytoskeletal regulatory protein binding(GO:0005519)
1.7	6.8	GO:0061628	H3K27me3 modified histone binding(GO:0061628)
0.2	6.8	GO:0005086	ARF guanyl-nucleotide exchange factor activity(GO:0005086)
0.3	6.4	GO:0034237	protein kinase A regulatory subunit binding(GO:0034237)
0.1	6.2	GO:0046875	ephrin receptor binding(GO:0046875)
1.0	6.1	GO:0061649	ubiquitinated histone binding(GO:0061649)
0.1	6.0	GO:0045182	translation regulator activity(GO:0045182)
0.1	5.7	GO:0005544	calcium-dependent phospholipid binding(GO:0005544)
1.3	5.4	GO:0030160	GKAP/Homer scaffold activity(GO:0030160)
0.5	5.3	GO:0030235	nitric-oxide synthase regulator activity(GO:0030235)
0.6	4.8	GO:0031811	G-protein coupled nucleotide receptor binding(GO:0031811) P2Y1 nucleotide receptor binding(GO:0031812)

Gene overrepresentation in C2:CP category:

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Showing 1 to 20 of 33 entries

Log-likelihood per target	Total log-likelihood	Term	Description
2.1	47.8	ST_WNT_CA2_CYCLIC_GMP_PATHWAY	Wnt/Ca2+/cyclic GMP signaling.
0.1	10.7	NABA_SECRETED_FACTORS	Genes encoding secreted soluble factors
0.3	9.1	ST_MYOCYTE_AD_PATHWAY	Myocyte Adrenergic Pathway is a specific case of the generalized Adrenergic Pathway.
0.1	9.1	NABA_ECM_AFFILIATED	Genes encoding proteins affiliated structurally or functionally to extracellular matrix proteins
0.1	8.3	PID_LKB1_PATHWAY	LKB1 signaling events
0.1	7.8	PID_NOTCH_PATHWAY	Notch signaling pathway
0.1	6.7	PID_RAC1_REG_PATHWAY	Regulation of RAC1 activity
0.1	4.9	PID_ECADHERIN_STABILIZATION_PATHWAY	Stabilization and expansion of the E-cadherin adherens junction
0.2	4.0	PID_RET_PATHWAY	Signaling events regulated by Ret tyrosine kinase
0.1	3.9	PID_FOXO_PATHWAY	FoxO family signaling
0.0	3.7	PID_P73PATHWAY	p73 transcription factor network
0.0	3.2	NABA_ECM_GLYCOPROTEINS	Genes encoding structural ECM glycoproteins
0.0	2.5	PID_CERAMIDE_PATHWAY	Ceramide signaling pathway
0.1	2.2	PID_NCADHERIN_PATHWAY	N-cadherin signaling events
0.1	2.2	SIG_REGULATION_OF_THE_ACTIN_CYTOSKELETON_BY_RHO_GTPASES	Genes related to regulation of the actin cytoskeleton
0.1	1.8	SA_G1_AND_S_PHASES	Cdk2, 4, and 6 bind cyclin D in G1, while cdk2/cyclin E promotes the G1/S transition.
0.1	1.7	PID_ARF6_PATHWAY	Arf6 signaling events
0.1	1.5	PID_IL8_CXCR1_PATHWAY	IL8- and CXCR1-mediated signaling events
0.0	1.5	PID_RAS_PATHWAY	Regulation of Ras family activation
0.0	1.5	PID_HEDGEHOG_GLI_PATHWAY	Hedgehog signaling events mediated by Gli proteins

Gene overrepresentation in C2:CP:REACTOME category:

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Showing 1 to 20 of 56 entries

Log-likelihood per target	Total log-likelihood	Term	Description
2.0	50.4	REACTOME_CREB_PHOSPHORYLATION_THROUGH_THE_ACTIVATION_OF_CAMKII	Genes involved in CREB phosphorylation through the activation of CaMKII
0.5	13.0	REACTOME_OTHER_SEMAPHORIN_INTERACTIONS	Genes involved in Other semaphorin interactions
0.1	9.5	REACTOME_REGULATION_OF_INSULIN_SECRETION	Genes involved in Regulation of Insulin Secretion
0.2	8.8	REACTOME_TRAFFICKING_OF_AMPA_RECEPTORS	Genes involved in Trafficking of AMPA receptors
0.2	6.7	REACTOME_INHIBITION_OF_VOLTAGE_GATED_CA2_CHANNELS_VIA_GBETA_GAMMA_SUBUNITS	Genes involved in Inhibition of voltage gated Ca2+ channels via Gbeta/gamma subunits
0.3	6.5	REACTOME_ACTIVATION_OF_BH3_ONLY_PROTEINS	Genes involved in Activation of BH3-only proteins
0.1	6.4	REACTOME_NRAGE_SIGNALS_DEATH_THROUGH_JNK	Genes involved in NRAGE signals death through JNK
0.1	5.0	REACTOME_ASSOCIATION_OF_TRIC_CCT_WITH_TARGET_PROTEINS_DURING_BIOSYNTHESIS	Genes involved in Association of TriC/CCT with target proteins during biosynthesis
0.1	4.7	REACTOME_SYNTHESIS_OF_PA	Genes involved in Synthesis of PA
0.2	4.4	REACTOME_CHEMOKINE_RECEPTORS_BIND_CHEMOKINES	Genes involved in Chemokine receptors bind chemokines
0.2	3.8	REACTOME_JNK_C_JUN_KINASES_PHOSPHORYLATION_AND_ACTIVATION_MEDIATED_BY_ACTIVATED_HUMAN_TAK1	Genes involved in JNK (c-Jun kinases) phosphorylation and activation mediated by activated human TAK1
0.3	3.7	REACTOME_HDL_MEDIATED_LIPID_TRANSPORT	Genes involved in HDL-mediated lipid transport
0.1	3.3	REACTOME_ACTIVATED_NOTCH1_TRANSMITS_SIGNAL_TO_THE_NUCLEUS	Genes involved in Activated NOTCH1 Transmits Signal to the Nucleus
0.2	3.0	REACTOME_POST_CHAPERONIN_TUBULIN_FOLDING_PATHWAY	Genes involved in Post-chaperonin tubulin folding pathway
0.1	2.9	REACTOME_MITOCHONDRIAL_PROTEIN_IMPORT	Genes involved in Mitochondrial Protein Import
0.1	2.6	REACTOME_KINESINS	Genes involved in Kinesins
0.3	2.4	REACTOME_FGFR4_LIGAND_BINDING_AND_ACTIVATION	Genes involved in FGFR4 ligand binding and activation
0.0	2.3	REACTOME_TRANSPORT_OF_INORGANIC_CATIONS_ANIONS_AND_AMINO_ACIDS_OLIGOPEPTIDES	Genes involved in Transport of inorganic cations/anions and amino acids/oligopeptides
0.2	2.2	REACTOME_NEF_MEDIATED_DOWNREGULATION_OF_MHC_CLASS_I_COMPLEX_CELL_SURFACE_EXPRESSION	Genes involved in Nef mediated downregulation of MHC class I complex cell surface expression
0.0	2.2	REACTOME_RESPIRATORY_ELECTRON_TRANSPORT_ATP_SYNTHESIS_BY_CHEMIOSMOTIC_COUPLING_AND_HEAT_PRODUCTION_BY_UNCOUPLING_PROTEINS_	Genes involved in Respiratory electron transport, ATP synthesis by chemiosmotic coupling, and heat production by uncoupling proteins.