ISMARA results: Rfx3_Rfx1

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GSE53960: rat RNA-Seq transcriptomic Bodymap

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Results for Rfx3_Rfx1_Rfx4

Z-value: 5.86

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Transcription factors associated with Rfx3_Rfx1_Rfx4

Gene Symbol	Gene ID	Gene Info
Rfx3 NCBI RGD Ensembl	ENSRNOG00000014486	regulatory factor X3
Rfx1 NCBI RGD Ensembl	ENSRNOG00000006049	regulatory factor X1
Rfx4 NCBI RGD Ensembl	ENSRNOG00000051536	regulatory factor X4

Activity-expression correlation:

Gene	Promoter	Pearson corr. coef.	P-value	Plot
Rfx4	rn6_v1_chr7_+_25832521_25832521	0.75	1.9e-58	Click!
Rfx3	rn6_v1_chr1_-_246010594_246010594	0.67	7.4e-43	Click!
Rfx1	rn6_v1_chr19_+_25181564_25181564	0.25	8.1e-06	Click!

Activity profile of Rfx3_Rfx1_Rfx4 motif

Sorted Z-values of Rfx3_Rfx1_Rfx4 motif

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Promoter	Log-likelihood	Transcript	Gene	Gene Info
chr5_-_138462864 Show fit	333.08	ENSRNOT00000011325	Ccdc30 NCBI RGD Ensembl Show fit	coiled-coil domain containing 30
chr8_-_65587427 Show fit	281.31	ENSRNOT00000016491	Lrrc49 NCBI RGD Ensembl Show fit	leucine rich repeat containing 49
chr7_+_139762614 Show fit	276.46	ENSRNOT00000031157	Ccdc184 NCBI RGD Ensembl Show fit	coiled-coil domain containing 184
chr8_-_65587658 Show fit	250.71	ENSRNOT00000091982	Lrrc49 NCBI RGD Ensembl Show fit	leucine rich repeat containing 49
chr3_+_113251778 Show fit	242.69	ENSRNOT00000083005	Map1a NCBI RGD Ensembl Show fit	microtubule-associated protein 1A
chr20_-_44220702 Show fit	236.11	ENSRNOT00000036853	Fam229b NCBI RGD Ensembl Show fit	family with sequence similarity 229, member B
chr20_-_14573519 Show fit	226.60	ENSRNOT00000001772	Rab36 NCBI RGD Ensembl Show fit	RAB36, member RAS oncogene family
chr16_+_2379480 Show fit	218.40	ENSRNOT00000079215	Dnah12 NCBI RGD Ensembl Show fit	dynein, axonemal, heavy chain 12
chr19_+_56010085 Show fit	213.81	ENSRNOT00000058216	Spata33 NCBI RGD Ensembl Show fit	spermatogenesis associated 33
chr5_+_140870140 Show fit	212.21	ENSRNOT00000074347	Hpcal4 NCBI RGD Ensembl Show fit	hippocalcin-like 4

Showing 1 to 10 of 200 entries

Network of associatons between targets according to the STRING database.

First level regulatory network of Rfx3_Rfx1_Rfx4

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Gene Ontology Analysis

Gene overrepresentation in biological process category:

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Log-likelihood per target	Total log-likelihood	Term	Description
4.7	884.2	GO:0060271	cilium morphogenesis(GO:0060271)
23.3	581.4	GO:0044458	motile cilium assembly(GO:0044458)
16.3	390.4	GO:0042073	intraciliary transport(GO:0042073)
25.6	358.9	GO:0060294	cilium movement involved in cell motility(GO:0060294)
16.7	333.6	GO:0048268	clathrin coat assembly(GO:0048268)
3.4	332.3	GO:1903955	positive regulation of establishment of protein localization to mitochondrion(GO:1903749) positive regulation of protein targeting to mitochondrion(GO:1903955)
10.0	329.8	GO:0010107	potassium ion import(GO:0010107)
23.5	328.4	GO:0007288	sperm axoneme assembly(GO:0007288)
2.1	312.4	GO:0007018	microtubule-based movement(GO:0007018)
5.4	265.2	GO:0071158	positive regulation of cell cycle arrest(GO:0071158)

Showing 1 to 10 of 247 entries

Gene overrepresentation in cellular component category:

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Log-likelihood per target	Total log-likelihood	Term	Description
21.0	734.1	GO:0030990	intraciliary transport particle(GO:0030990)
13.7	672.6	GO:0030286	dynein complex(GO:0030286)
9.6	623.2	GO:0036126	sperm flagellum(GO:0036126)
1.5	445.3	GO:0030659	cytoplasmic vesicle membrane(GO:0030659)
2.7	408.8	GO:0005929	cilium(GO:0005929)
1.4	393.2	GO:0014069	postsynaptic density(GO:0014069)
6.1	357.0	GO:0005930	axoneme(GO:0005930) ciliary plasm(GO:0097014)
0.4	344.3	GO:0005887	integral component of plasma membrane(GO:0005887)
14.0	335.3	GO:0034451	centriolar satellite(GO:0034451)
17.3	294.7	GO:0035686	sperm fibrous sheath(GO:0035686)

Showing 1 to 10 of 131 entries

Gene overrepresentation in molecular function category:

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Log-likelihood per target	Total log-likelihood	Term	Description
10.1	795.5	GO:0003777	microtubule motor activity(GO:0003777)
3.0	578.1	GO:0008017	microtubule binding(GO:0008017)
1.8	493.1	GO:0003924	GTPase activity(GO:0003924)
1.8	386.0	GO:0004866	endopeptidase inhibitor activity(GO:0004866)
0.6	313.9	GO:0005509	calcium ion binding(GO:0005509)
49.3	296.0	GO:0032051	clathrin light chain binding(GO:0032051)
18.9	226.9	GO:0003841	1-acylglycerol-3-phosphate O-acyltransferase activity(GO:0003841)
7.8	225.0	GO:0004693	cyclin-dependent protein serine/threonine kinase activity(GO:0004693)
4.0	221.0	GO:0051018	protein kinase A binding(GO:0051018)
1.4	220.5	GO:0017137	Rab GTPase binding(GO:0017137)

Showing 1 to 10 of 163 entries

Gene overrepresentation in curated gene sets: canonical pathways category:

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Log-likelihood per target	Total log-likelihood	Term	Description
9.2	375.6	ST ADRENERGIC	Adrenergic Pathway
5.0	277.9	PID HEDGEHOG GLI PATHWAY	Hedgehog signaling events mediated by Gli proteins
11.5	195.4	SA REG CASCADE OF CYCLIN EXPR	Expression of cyclins regulates progression through the cell cycle by activating cyclin-dependent kinases.
10.5	167.5	ST WNT CA2 CYCLIC GMP PATHWAY	Wnt/Ca2+/cyclic GMP signaling.
2.0	142.8	PID E2F PATHWAY	E2F transcription factor network
0.7	140.7	NABA ECM GLYCOPROTEINS	Genes encoding structural ECM glycoproteins
2.0	135.1	PID BETA CATENIN NUC PATHWAY	Regulation of nuclear beta catenin signaling and target gene transcription
3.0	106.1	PID RAS PATHWAY	Regulation of Ras family activation
2.0	98.1	PID PLK1 PATHWAY	PLK1 signaling events
1.9	82.8	PID INTEGRIN A4B1 PATHWAY	Alpha4 beta1 integrin signaling events

Showing 1 to 10 of 43 entries

Gene overrepresentation in curated gene sets: REACTOME pathways category:

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Log-likelihood per target	Total log-likelihood	Term	Description
11.0	373.5	REACTOME TRAFFICKING OF AMPA RECEPTORS	Genes involved in Trafficking of AMPA receptors
11.0	329.8	REACTOME INHIBITION OF VOLTAGE GATED CA2 CHANNELS VIA GBETA GAMMA SUBUNITS	Genes involved in Inhibition of voltage gated Ca2+ channels via Gbeta/gamma subunits
2.3	260.4	REACTOME TRANSPORT OF INORGANIC CATIONS ANIONS AND AMINO ACIDS OLIGOPEPTIDES	Genes involved in Transport of inorganic cations/anions and amino acids/oligopeptides
7.7	245.5	REACTOME SYNTHESIS OF PA	Genes involved in Synthesis of PA
12.2	195.4	REACTOME CYCLIN A B1 ASSOCIATED EVENTS DURING G2 M TRANSITION	Genes involved in Cyclin A/B1 associated events during G2/M transition
0.8	178.1	REACTOME ANTIGEN PROCESSING UBIQUITINATION PROTEASOME DEGRADATION	Genes involved in Antigen processing: Ubiquitination & Proteasome degradation
10.0	170.3	REACTOME RAP1 SIGNALLING	Genes involved in Rap1 signalling
10.3	165.0	REACTOME ACTIVATION OF THE AP1 FAMILY OF TRANSCRIPTION FACTORS	Genes involved in Activation of the AP-1 family of transcription factors
7.5	150.0	REACTOME PKA MEDIATED PHOSPHORYLATION OF CREB	Genes involved in PKA-mediated phosphorylation of CREB
2.7	138.9	REACTOME VOLTAGE GATED POTASSIUM CHANNELS	Genes involved in Voltage gated Potassium channels

Showing 1 to 10 of 53 entries

Results for Rfx3_Rfx1_Rfx4

Z-value: 5.86

Motif logo

Transcription factors associated with Rfx3_Rfx1_Rfx4

Activity-expression correlation:

Activity profile of Rfx3_Rfx1_Rfx4 motif

Sorted Z-values of Rfx3_Rfx1_Rfx4 motif

Top targets:

Network of associatons between targets according to the STRING database.

First level regulatory network of Rfx3_Rfx1_Rfx4

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Gene Ontology Analysis

Gene overrepresentation in biological process category:

Gene overrepresentation in cellular component category:

Gene overrepresentation in molecular function category:

Gene overrepresentation in curated gene sets: canonical pathways category:

Gene overrepresentation in curated gene sets: REACTOME pathways category: