ISMARA results: rfx3

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PRJDB7713: Age associated transcriptome analysis in 5 tissues of zebrafish

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Results for rfx3_rfx2+rfx4

Z-value: 4.31

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Transcription factors associated with rfx3_rfx2+rfx4

Gene Symbol	Gene ID	Gene Info
rfx3 NCBI UniProt	ENSDARG00000014550	regulatory factor X, 3 (influences HLA class II expression)
rfx2 NCBI UniProt	ENSDARG00000013575	regulatory factor X, 2 (influences HLA class II expression)
rfx4 NCBI UniProt	ENSDARG00000026395	regulatory factor X, 4
rfx4 NCBI UniProt	ENSDARG00000116861	regulatory factor X, 4

Activity-expression correlation:

Gene	Promoter	Pearson corr. coef.	P-value	Plot
rfx4	dr11_v1_chr18_-_15373620_15373620	0.79	4.8e-21	Click!
rfx3	dr11_v1_chr10_-_641609_641609	0.49	4.5e-07	Click!
rfx2	dr11_v1_chr8_-_20138054_20138251	-0.13	2.0e-01	Click!

Activity profile of rfx3_rfx2+rfx4 motif

Sorted Z-values of rfx3_rfx2+rfx4 motif

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Promoter	Log-likelihood	Transcript	Gene	Gene Info
chr21_+_26697536 Show fit	61.23	ENSDART00000004109	gng3 NCBI UniProt Show fit	guanine nucleotide binding protein (G protein), gamma 3
chr19_-_9472893 Show fit	55.81	ENSDART00000045565 ENSDART00000137505	vamp1 NCBI UniProt Show fit	vesicle-associated membrane protein 1
chr20_-_9436521 Show fit	52.27	ENSDART00000133000	zgc:101840 NCBI UniProt Show fit	zgc:101840
chr17_-_6759006 Show fit	46.03	ENSDART00000184692 ENSDART00000180530	vsnl1b NCBI UniProt Show fit	visinin-like 1b
chr24_-_24163201 Show fit	42.43	ENSDART00000140170	map7d2b NCBI UniProt Show fit	MAP7 domain containing 2b
chr23_-_19953089 Show fit	40.88	ENSDART00000153828	atp2b3b NCBI UniProt Show fit	ATPase plasma membrane Ca2+ transporting 3b
chr5_+_32162684 Show fit	39.43	ENSDART00000134472	taok3b NCBI UniProt Show fit	TAO kinase 3b
chr5_-_23317477 Show fit	38.88	ENSDART00000090171	nlgn3b NCBI UniProt Show fit	neuroligin 3b
chr10_-_35542071 Show fit	38.85	ENSDART00000162139	si:ch211-244c8.4 NCBI UniProt Show fit	si:ch211-244c8.4
chr13_-_36911118 Show fit	38.73	ENSDART00000048739	trim9 NCBI UniProt Show fit	tripartite motif containing 9

Showing 1 to 10 of 200 entries

Network of associatons between targets according to the STRING database.

First level regulatory network of rfx3_rfx2+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
0.2	71.3	GO:0000226	microtubule cytoskeleton organization(GO:0000226)
0.1	70.0	GO:0006397	mRNA processing(GO:0006397)
2.3	61.1	GO:0031114	regulation of microtubule depolymerization(GO:0031114)
0.3	58.1	GO:0071805	cellular potassium ion transport(GO:0071804) potassium ion transmembrane transport(GO:0071805)
3.7	55.8	GO:0035493	SNARE complex assembly(GO:0035493)
5.2	52.0	GO:0021631	optic nerve morphogenesis(GO:0021631)
1.2	49.8	GO:1903670	regulation of sprouting angiogenesis(GO:1903670)
2.3	48.5	GO:0007019	microtubule depolymerization(GO:0007019)
0.2	44.4	GO:0006470	protein dephosphorylation(GO:0006470)
0.1	41.3	GO:0007010	cytoskeleton organization(GO:0007010)

Showing 1 to 10 of 184 entries

Gene overrepresentation in cellular component category:

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Log-likelihood per target	Total log-likelihood	Term	Description
1.0	127.7	GO:0043025	neuronal cell body(GO:0043025)
0.4	104.5	GO:0005929	cilium(GO:0005929)
0.2	97.4	GO:0043005	neuron projection(GO:0043005)
0.3	86.3	GO:0005874	microtubule(GO:0005874)
0.2	81.3	GO:0015630	microtubule cytoskeleton(GO:0015630)
0.1	81.2	GO:0005887	integral component of plasma membrane(GO:0005887)
0.1	71.2	GO:0005789	endoplasmic reticulum membrane(GO:0005789)
0.9	68.9	GO:0030141	secretory granule(GO:0030141)
3.6	61.2	GO:0031680	G-protein beta/gamma-subunit complex(GO:0031680)
0.2	51.6	GO:0045202	synapse(GO:0045202)

Showing 1 to 10 of 80 entries

Gene overrepresentation in molecular function category:

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Log-likelihood per target	Total log-likelihood	Term	Description
0.4	155.4	GO:0015631	tubulin binding(GO:0015631)
0.4	128.3	GO:0003924	GTPase activity(GO:0003924)
0.0	92.0	GO:0000981	RNA polymerase II transcription factor activity, sequence-specific DNA binding(GO:0000981)
2.0	78.8	GO:0017075	syntaxin-1 binding(GO:0017075)
0.2	73.7	GO:0061630	ubiquitin protein ligase activity(GO:0061630)
0.2	68.9	GO:0030695	GTPase regulator activity(GO:0030695)
0.5	68.8	GO:0005516	calmodulin binding(GO:0005516)
2.9	61.2	GO:0031681	G-protein beta-subunit binding(GO:0031681)
1.0	58.1	GO:0005200	structural constituent of cytoskeleton(GO:0005200)
0.2	50.6	GO:0004721	phosphoprotein phosphatase activity(GO:0004721)

Showing 1 to 10 of 126 entries

Gene overrepresentation in curated gene sets: canonical pathways category:

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Log-likelihood per target	Total log-likelihood	Term	Description
0.9	36.2	PID ILK PATHWAY	Integrin-linked kinase signaling
0.8	27.7	ST DIFFERENTIATION PATHWAY IN PC12 CELLS	Differentiation Pathway in PC12 Cells; this is a specific case of PAC1 Receptor Pathway.
1.4	26.9	ST WNT CA2 CYCLIC GMP PATHWAY	Wnt/Ca2+/cyclic GMP signaling.
1.0	25.3	PID IGF1 PATHWAY	IGF1 pathway
0.3	11.7	PID ATM PATHWAY	ATM pathway
0.3	11.4	PID IL12 2PATHWAY	IL12-mediated signaling events
0.4	10.5	PID MYC PATHWAY	C-MYC pathway
0.1	9.4	NABA ECM REGULATORS	Genes encoding enzymes and their regulators involved in the remodeling of the extracellular matrix
0.4	6.9	PID LIS1 PATHWAY	Lissencephaly gene (LIS1) in neuronal migration and development
0.2	6.7	PID FRA PATHWAY	Validated transcriptional targets of AP1 family members Fra1 and Fra2

Showing 1 to 10 of 17 entries

Gene overrepresentation in curated gene sets: REACTOME pathways category:

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Log-likelihood per target	Total log-likelihood	Term	Description
3.6	61.2	REACTOME INHIBITION OF INSULIN SECRETION BY ADRENALINE NORADRENALINE	Genes involved in Inhibition of Insulin Secretion by Adrenaline/Noradrenaline
3.4	58.3	REACTOME PROTEOLYTIC CLEAVAGE OF SNARE COMPLEX PROTEINS	Genes involved in Proteolytic cleavage of SNARE complex proteins
12.2	36.6	REACTOME CREB PHOSPHORYLATION THROUGH THE ACTIVATION OF CAMKII	Genes involved in CREB phosphorylation through the activation of CaMKII
0.2	35.7	REACTOME ANTIGEN PROCESSING UBIQUITINATION PROTEASOME DEGRADATION	Genes involved in Antigen processing: Ubiquitination & Proteasome degradation
2.0	32.1	REACTOME POST CHAPERONIN TUBULIN FOLDING PATHWAY	Genes involved in Post-chaperonin tubulin folding pathway
0.8	24.4	REACTOME SPHINGOLIPID DE NOVO BIOSYNTHESIS	Genes involved in Sphingolipid de novo biosynthesis
0.6	21.5	REACTOME VOLTAGE GATED POTASSIUM CHANNELS	Genes involved in Voltage gated Potassium channels
1.1	19.7	REACTOME SYNTHESIS OF GLYCOSYLPHOSPHATIDYLINOSITOL GPI	Genes involved in Synthesis of glycosylphosphatidylinositol (GPI)
0.2	17.2	REACTOME FACTORS INVOLVED IN MEGAKARYOCYTE DEVELOPMENT AND PLATELET PRODUCTION	Genes involved in Factors involved in megakaryocyte development and platelet production
0.7	16.1	REACTOME GLUCONEOGENESIS	Genes involved in Gluconeogenesis

Showing 1 to 10 of 28 entries

Results for rfx3_rfx2+rfx4

Z-value: 4.31

Motif logo

Transcription factors associated with rfx3_rfx2+rfx4

Activity-expression correlation:

Activity profile of rfx3_rfx2+rfx4 motif

Sorted Z-values of rfx3_rfx2+rfx4 motif

Top targets:

Network of associatons between targets according to the STRING database.

First level regulatory network of rfx3_rfx2+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: