ISMARA results: nkx3-1

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PRJNA438478: RNAseq of wild type zebrafish germline

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Results for nkx3-1

Z-value: 1.03

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Transcription factors associated with nkx3-1

Gene Symbol	Gene ID	Gene Info
nkx3-1 NCBI UniProt	ENSDARG00000078280	NK3 homeobox 1

Activity-expression correlation:

Gene	Promoter	Pearson corr. coef.	P-value	Plot
nkx3-1	dr11_v1_chr8_-_50259448_50259448	-0.90	3.1e-07	Click!

Activity profile of nkx3-1 motif

Sorted Z-values of nkx3-1 motif

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Promoter	Log-likelihood	Transcript	Gene	Gene Info
chr9_+_8396755 Show fit	5.57	ENSDART00000043067	zgc:171776 NCBI UniProt Show fit	zgc:171776
chr22_+_25236657 Show fit	5.41	ENSDART00000138012	zgc:172218 NCBI UniProt Show fit	zgc:172218
chr5_+_16117871 Show fit	4.70	ENSDART00000090657	znrf3 NCBI UniProt Show fit	zinc and ring finger 3
chr9_+_44994214 Show fit	4.52	ENSDART00000141434	retsatl NCBI UniProt Show fit	retinol saturase (all-trans-retinol 13,14-reductase) like
chr22_+_25249193 Show fit	4.16	ENSDART00000171851	si:ch211-226h8.11 NCBI UniProt Show fit	si:ch211-226h8.11
chr10_-_34915886 Show fit	3.37	ENSDART00000141201 ENSDART00000002166	ccna1 NCBI UniProt Show fit	cyclin A1
chr10_-_34916208 Show fit	3.08	ENSDART00000187371	ccna1 NCBI UniProt Show fit	cyclin A1
chr7_+_17947217 Show fit	2.74	ENSDART00000101601	cth1 NCBI UniProt Show fit	cysteine three histidine 1
chr15_+_29025090 Show fit	1.97	ENSDART00000131755	si:ch211-137a8.2 NCBI UniProt Show fit	si:ch211-137a8.2
chr3_-_31875138 Show fit	1.96	ENSDART00000155298	limd2 NCBI UniProt Show fit	LIM domain containing 2

Showing 1 to 10 of 200 entries

Network of associatons between targets according to the STRING database.

First level regulatory network of nkx3-1

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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
0.1	4.9	GO:0000079	regulation of cyclin-dependent protein serine/threonine kinase activity(GO:0000079) regulation of cyclin-dependent protein kinase activity(GO:1904029)
1.2	4.7	GO:0032801	receptor catabolic process(GO:0032801)
0.1	3.2	GO:0030488	tRNA methylation(GO:0030488)
0.1	2.5	GO:0006506	GPI anchor biosynthetic process(GO:0006506)
0.1	2.2	GO:0048264	determination of ventral identity(GO:0048264)
0.0	2.1	GO:0045930	negative regulation of mitotic cell cycle(GO:0045930)
0.3	2.0	GO:0032367	intracellular cholesterol transport(GO:0032367)
0.2	1.9	GO:0045835	negative regulation of meiotic nuclear division(GO:0045835)
0.1	1.9	GO:0044773	mitotic DNA damage checkpoint(GO:0044773)
0.1	1.8	GO:0016926	protein desumoylation(GO:0016926)

Showing 1 to 10 of 86 entries

Gene overrepresentation in cellular component category:

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Log-likelihood per target	Total log-likelihood	Term	Description
2.2	6.5	GO:0097124	cyclin A2-CDK2 complex(GO:0097124)
0.0	3.9	GO:0005764	lysosome(GO:0005764)
0.1	2.8	GO:0071141	SMAD protein complex(GO:0071141)
0.4	2.5	GO:0000506	glycosylphosphatidylinositol-N-acetylglucosaminyltransferase (GPI-GnT) complex(GO:0000506)
0.1	2.0	GO:0034992	microtubule organizing center attachment site(GO:0034992) LINC complex(GO:0034993)
0.2	1.7	GO:0090533	sodium:potassium-exchanging ATPase complex(GO:0005890) cation-transporting ATPase complex(GO:0090533)
0.1	1.7	GO:0044665	MLL1/2 complex(GO:0044665) MLL1 complex(GO:0071339)
0.0	1.6	GO:0055038	recycling endosome membrane(GO:0055038)
0.4	1.5	GO:0060171	stereocilium membrane(GO:0060171)
0.1	1.3	GO:0017119	Golgi transport complex(GO:0017119)

Showing 1 to 10 of 35 entries

Gene overrepresentation in molecular function category:

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Log-likelihood per target	Total log-likelihood	Term	Description
0.1	17.3	GO:0030246	carbohydrate binding(GO:0030246)
0.0	6.4	GO:0004842	ubiquitin-protein transferase activity(GO:0004842)
0.1	4.9	GO:0016538	cyclin-dependent protein serine/threonine kinase regulator activity(GO:0016538)
0.1	3.2	GO:0032934	sterol binding(GO:0032934)
0.4	2.5	GO:0017176	phosphatidylinositol N-acetylglucosaminyltransferase activity(GO:0017176)
0.1	2.1	GO:0070411	I-SMAD binding(GO:0070411)
0.6	1.8	GO:0016300	tRNA (uracil) methyltransferase activity(GO:0016300)
0.1	1.8	GO:0016929	SUMO-specific protease activity(GO:0016929)
0.0	1.8	GO:0003727	single-stranded RNA binding(GO:0003727)
0.1	1.7	GO:0001671	ATPase activator activity(GO:0001671)

Showing 1 to 10 of 70 entries

Gene overrepresentation in curated gene sets: canonical pathways category:

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Log-likelihood per target	Total log-likelihood	Term	Description
0.4	6.5	SA REG CASCADE OF CYCLIN EXPR	Expression of cyclins regulates progression through the cell cycle by activating cyclin-dependent kinases.
0.1	1.7	PID ATM PATHWAY	ATM pathway
0.0	1.5	PID KIT PATHWAY	Signaling events mediated by Stem cell factor receptor (c-Kit)
0.1	1.0	PID RANBP2 PATHWAY	Sumoylation by RanBP2 regulates transcriptional repression
0.0	0.9	PID DNA PK PATHWAY	DNA-PK pathway in nonhomologous end joining
0.0	0.8	PID DELTA NP63 PATHWAY	Validated transcriptional targets of deltaNp63 isoforms
0.0	0.7	PID INSULIN GLUCOSE PATHWAY	Insulin-mediated glucose transport
0.0	0.4	PID ARF 3PATHWAY	Arf1 pathway
0.0	0.4	PID PI3KCI AKT PATHWAY	Class I PI3K signaling events mediated by Akt
0.0	0.4	SIG REGULATION OF THE ACTIN CYTOSKELETON BY RHO GTPASES	Genes related to regulation of the actin cytoskeleton

Showing 1 to 10 of 12 entries

Gene overrepresentation in curated gene sets: REACTOME pathways category:

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Log-likelihood per target	Total log-likelihood	Term	Description
0.4	6.5	REACTOME CYCLIN A B1 ASSOCIATED EVENTS DURING G2 M TRANSITION	Genes involved in Cyclin A/B1 associated events during G2/M transition
0.1	2.5	REACTOME SYNTHESIS OF GLYCOSYLPHOSPHATIDYLINOSITOL GPI	Genes involved in Synthesis of glycosylphosphatidylinositol (GPI)
0.3	1.9	REACTOME G2 M DNA DAMAGE CHECKPOINT	Genes involved in G2/M DNA damage checkpoint
0.0	1.6	REACTOME GLYCOSPHINGOLIPID METABOLISM	Genes involved in Glycosphingolipid metabolism
0.0	1.5	REACTOME SYNTHESIS OF PIPS AT THE PLASMA MEMBRANE	Genes involved in Synthesis of PIPs at the plasma membrane
0.1	1.3	REACTOME PRE NOTCH PROCESSING IN GOLGI	Genes involved in Pre-NOTCH Processing in Golgi
0.0	1.3	REACTOME PYRUVATE METABOLISM AND CITRIC ACID TCA CYCLE	Genes involved in Pyruvate metabolism and Citric Acid (TCA) cycle
0.0	1.2	REACTOME TRANSPORT OF INORGANIC CATIONS ANIONS AND AMINO ACIDS OLIGOPEPTIDES	Genes involved in Transport of inorganic cations/anions and amino acids/oligopeptides
0.3	1.1	REACTOME REGULATION OF COMPLEMENT CASCADE	Genes involved in Regulation of Complement cascade
0.0	1.1	REACTOME MRNA SPLICING MINOR PATHWAY	Genes involved in mRNA Splicing - Minor Pathway

Showing 1 to 10 of 26 entries

Results for nkx3-1

Z-value: 1.03

Motif logo

Transcription factors associated with nkx3-1

Activity-expression correlation:

Activity profile of nkx3-1 motif

Sorted Z-values of nkx3-1 motif

Top targets:

Network of associatons between targets according to the STRING database.

First level regulatory network of nkx3-1

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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: