ISMARA results: vsx1_shox_shox2_uncx4.1

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PRJNA438478: RNAseq of wild type zebrafish germline

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Results for vsx1_shox_shox2_uncx4.1_lhx2a

Z-value: 1.15

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Transcription factors associated with vsx1_shox_shox2_uncx4.1_lhx2a

Gene Symbol	Gene ID	Gene Info
vsx1 NCBI UniProt	ENSDARG00000056292	visual system homeobox 1 homolog, chx10-like
vsx1 NCBI UniProt	ENSDARG00000109766	visual system homeobox 1 homolog, chx10-like
shox NCBI UniProt	ENSDARG00000025891	short stature homeobox
shox2 NCBI UniProt	ENSDARG00000075713	short stature homeobox 2
uncx4.1 NCBI UniProt	ENSDARG00000037760	Unc4.1 homeobox (C. elegans)
lhx2a NCBI UniProt	ENSDARG00000037964	LIM homeobox 2a

Activity-expression correlation:

Gene	Promoter	Pearson corr. coef.	P-value	Plot
lhx2a	dr11_v1_chr21_-_8422351_8422363	-0.98	1.7e-12	Click!
uncx4.1	dr11_v1_chr1_+_9290103_9290103	0.87	2.3e-06	Click!
shox	dr11_v1_chr9_+_34641237_34641237	-0.86	5.6e-06	Click!
vsx1	dr11_v1_chr17_-_21066075_21066105	-0.61	7.7e-03	Click!
shox2	dr11_v1_chr15_-_2188332_2188422	-0.19	4.4e-01	Click!

Activity profile of vsx1_shox_shox2_uncx4.1_lhx2a motif

Sorted Z-values of vsx1_shox_shox2_uncx4.1_lhx2a motif

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Promoter	Log-likelihood	Transcript	Gene	Gene Info
chr10_-_21362071 Show fit	10.19	ENSDART00000125167	avd NCBI UniProt Show fit	avidin
chr10_-_21362320 Show fit	9.54	ENSDART00000189789	avd NCBI UniProt Show fit	avidin
chr18_-_40708537 Show fit	9.27	ENSDART00000077577	si:ch211-132b12.8 NCBI UniProt Show fit	si:ch211-132b12.8
chr21_+_25777425 Show fit	9.20	ENSDART00000021620	cldnd NCBI UniProt Show fit	claudin d
chr11_-_6452444 Show fit	8.76	ENSDART00000137879 ENSDART00000134957 ENSDART00000004483	larp6b NCBI UniProt Show fit	La ribonucleoprotein domain family, member 6b
chr8_+_45334255 Show fit	7.14	ENSDART00000126848 ENSDART00000134161 ENSDART00000142322 ENSDART00000145011 ENSDART00000183560	pabpc1l NCBI UniProt Show fit	poly(A) binding protein, cytoplasmic 1-like
chr16_+_29509133 Show fit	7.11	ENSDART00000112116	ctss2.1 NCBI UniProt Show fit	cathepsin S, ortholog2, tandem duplicate 1
chr20_-_23426339 Show fit	6.83	ENSDART00000004625	zar1 NCBI UniProt Show fit	zygote arrest 1
chr9_-_35633827 Show fit	6.75	ENSDART00000077745	zp2l1 NCBI UniProt Show fit	zona pellucida glycoprotein 2, like 1
chr11_-_44801968 Show fit	6.67	ENSDART00000161846	map1lc3c NCBI UniProt Show fit	microtubule-associated protein 1 light chain 3 gamma

Showing 1 to 10 of 200 entries

Network of associatons between targets according to the STRING database.

First level regulatory network of vsx1_shox_shox2_uncx4.1_lhx2a

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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
0.7	12.4	GO:0035803	binding of sperm to zona pellucida(GO:0007339) egg coat formation(GO:0035803) regulation of acrosome reaction(GO:0060046) positive regulation of acrosome reaction(GO:2000344)
1.8	9.2	GO:0016338	calcium-independent cell-cell adhesion via plasma membrane cell-adhesion molecules(GO:0016338)
0.2	9.0	GO:1904029	regulation of cyclin-dependent protein serine/threonine kinase activity(GO:0000079) regulation of cyclin-dependent protein kinase activity(GO:1904029)
0.1	8.9	GO:0017148	negative regulation of translation(GO:0017148)
0.3	6.6	GO:0043562	cellular response to nitrogen starvation(GO:0006995) cellular response to nitrogen levels(GO:0043562)
0.5	5.7	GO:0006607	NLS-bearing protein import into nucleus(GO:0006607)
0.1	4.9	GO:0018198	peptidyl-cysteine modification(GO:0018198)
1.5	4.5	GO:0072111	spinal cord anterior/posterior patterning(GO:0021512) cell proliferation involved in pronephros development(GO:0039015) cell proliferation involved in kidney development(GO:0072111)
0.1	4.5	GO:0042761	very long-chain fatty acid biosynthetic process(GO:0042761)
1.1	4.3	GO:0035124	embryonic caudal fin morphogenesis(GO:0035124)

Showing 1 to 10 of 153 entries

Gene overrepresentation in cellular component category:

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Log-likelihood per target	Total log-likelihood	Term	Description
0.1	14.1	GO:0005923	bicellular tight junction(GO:0005923) occluding junction(GO:0070160)
3.3	10.0	GO:0097124	cyclin A2-CDK2 complex(GO:0097124)
0.0	9.3	GO:0031012	extracellular matrix(GO:0031012)
0.2	7.5	GO:0000421	autophagosome membrane(GO:0000421)
0.0	6.6	GO:0000323	lytic vacuole(GO:0000323)
0.2	5.4	GO:0010494	cytoplasmic stress granule(GO:0010494)
1.5	4.5	GO:0097189	apoptotic body(GO:0097189)
0.9	4.3	GO:0070724	BMP receptor complex(GO:0070724)
0.2	3.8	GO:0042555	MCM complex(GO:0042555)
0.0	3.5	GO:0005730	nucleolus(GO:0005730)

Showing 1 to 10 of 68 entries

Gene overrepresentation in molecular function category:

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Log-likelihood per target	Total log-likelihood	Term	Description
3.9	19.7	GO:0009374	biotin binding(GO:0009374)
0.1	15.7	GO:0042802	identical protein binding(GO:0042802)
0.7	12.4	GO:0032190	acrosin binding(GO:0032190)
0.0	10.3	GO:0044822	mRNA binding(GO:0003729) poly(A) RNA binding(GO:0044822)
0.1	9.0	GO:0016538	cyclin-dependent protein serine/threonine kinase regulator activity(GO:0016538)
0.5	7.0	GO:0008266	poly(U) RNA binding(GO:0008266)
0.0	6.9	GO:0004197	cysteine-type endopeptidase activity(GO:0004197)
0.4	6.4	GO:0061608	nuclear import signal receptor activity(GO:0061608)
0.1	6.1	GO:0031625	ubiquitin protein ligase binding(GO:0031625)
0.1	5.3	GO:0005044	scavenger receptor activity(GO:0005044)

Showing 1 to 10 of 113 entries

Gene overrepresentation in curated gene sets: canonical pathways category:

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Log-likelihood per target	Total log-likelihood	Term	Description
0.6	10.0	SA REG CASCADE OF CYCLIN EXPR	Expression of cyclins regulates progression through the cell cycle by activating cyclin-dependent kinases.
0.1	6.8	WNT SIGNALING	Genes related to Wnt-mediated signal transduction
0.1	3.5	NABA COLLAGENS	Genes encoding collagen proteins
0.0	2.1	PID TELOMERASE PATHWAY	Regulation of Telomerase
0.1	1.6	PID HIF2PATHWAY	HIF-2-alpha transcription factor network
0.1	1.4	PID TCR CALCIUM PATHWAY	Calcium signaling in the CD4+ TCR pathway
0.0	1.3	PID HDAC CLASSI PATHWAY	Signaling events mediated by HDAC Class I
0.1	1.2	PID ECADHERIN KERATINOCYTE PATHWAY	E-cadherin signaling in keratinocytes
0.0	1.2	PID AURORA B PATHWAY	Aurora B signaling
0.0	0.9	NABA PROTEOGLYCANS	Genes encoding proteoglycans

Showing 1 to 10 of 20 entries

Gene overrepresentation in curated gene sets: REACTOME pathways category:

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Log-likelihood per target	Total log-likelihood	Term	Description
0.6	10.0	REACTOME CYCLIN A B1 ASSOCIATED EVENTS DURING G2 M TRANSITION	Genes involved in Cyclin A/B1 associated events during G2/M transition
0.1	3.5	REACTOME GLUCONEOGENESIS	Genes involved in Gluconeogenesis
0.1	3.5	REACTOME COLLAGEN FORMATION	Genes involved in Collagen formation
0.1	2.7	REACTOME BIOSYNTHESIS OF THE N GLYCAN PRECURSOR DOLICHOL LIPID LINKED OLIGOSACCHARIDE LLO AND TRANSFER TO A NASCENT PROTEIN	Genes involved in Biosynthesis of the N-glycan precursor (dolichol lipid-linked oligosaccharide, LLO) and transfer to a nascent protein
0.1	1.7	REACTOME PACKAGING OF TELOMERE ENDS	Genes involved in Packaging Of Telomere Ends
0.0	1.7	REACTOME ACTIVATION OF CHAPERONE GENES BY XBP1S	Genes involved in Activation of Chaperone Genes by XBP1(S)
0.0	1.6	REACTOME ION TRANSPORT BY P TYPE ATPASES	Genes involved in Ion transport by P-type ATPases
0.0	1.4	REACTOME MITOCHONDRIAL PROTEIN IMPORT	Genes involved in Mitochondrial Protein Import
0.0	1.3	REACTOME ELONGATION ARREST AND RECOVERY	Genes involved in Elongation arrest and recovery
0.0	1.2	REACTOME METABOLISM OF NON CODING RNA	Genes involved in Metabolism of non-coding RNA

Showing 1 to 10 of 36 entries

Results for vsx1_shox_shox2_uncx4.1_lhx2a

Z-value: 1.15

Motif logo

Transcription factors associated with vsx1_shox_shox2_uncx4.1_lhx2a

Activity-expression correlation:

Activity profile of vsx1_shox_shox2_uncx4.1_lhx2a motif

Sorted Z-values of vsx1_shox_shox2_uncx4.1_lhx2a motif

Top targets:

Network of associatons between targets according to the STRING database.

First level regulatory network of vsx1_shox_shox2_uncx4.1_lhx2a

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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: