ISMARA results: en1b_en2a+en2b_gbx1

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PRJNA438478: RNAseq of wild type zebrafish germline

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Results for en1b_en2a+en2b_gbx1_emx1

Z-value: 0.78

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Transcription factors associated with en1b_en2a+en2b_gbx1_emx1

Gene Symbol	Gene ID	Gene Info
en1b NCBI UniProt	ENSDARG00000098730	engrailed homeobox 1b
en2a NCBI UniProt	ENSDARG00000026599	engrailed homeobox 2a
en2b NCBI UniProt	ENSDARG00000038868	engrailed homeobox 2b
en2a NCBI UniProt	ENSDARG00000115233	engrailed homeobox 2a
gbx1 NCBI UniProt	ENSDARG00000071418	gastrulation brain homeobox 1
emx1 NCBI UniProt	ENSDARG00000039569	empty spiracles homeobox 1

Activity-expression correlation:

Gene	Promoter	Pearson corr. coef.	P-value	Plot
en2a	dr11_v1_chr7_-_40993456_40993456	-0.96	3.0e-10	Click!
en2b	dr11_v1_chr2_+_29976419_29976419	-0.96	5.1e-10	Click!
en1b	dr11_v1_chr1_+_7679328_7679328	-0.86	4.6e-06	Click!
emx1	dr11_v1_chr13_+_15004398_15004398	0.36	1.4e-01	Click!
gbx1	dr11_v1_chr24_+_34113424_34113424	-0.26	3.1e-01	Click!

Activity profile of en1b_en2a+en2b_gbx1_emx1 motif

Sorted Z-values of en1b_en2a+en2b_gbx1_emx1 motif

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Promoter	Log-likelihood	Transcript	Gene	Gene Info
chr21_+_25777425 Show fit	6.91	ENSDART00000021620	cldnd NCBI UniProt Show fit	claudin d
chr9_-_35633827 Show fit	5.50	ENSDART00000077745	zp2l1 NCBI UniProt Show fit	zona pellucida glycoprotein 2, like 1
chr10_-_21362071 Show fit	5.46	ENSDART00000125167	avd NCBI UniProt Show fit	avidin
chr10_-_21362320 Show fit	5.11	ENSDART00000189789	avd NCBI UniProt Show fit	avidin
chr20_-_23426339 Show fit	4.64	ENSDART00000004625	zar1 NCBI UniProt Show fit	zygote arrest 1
chr1_-_55248496 Show fit	4.02	ENSDART00000098615	nanos3 NCBI UniProt Show fit	nanos homolog 3
chr18_-_40708537 Show fit	3.98	ENSDART00000077577	si:ch211-132b12.8 NCBI UniProt Show fit	si:ch211-132b12.8
chr6_+_21001264 Show fit	3.77	ENSDART00000044519 ENSDART00000151278	cx44.2 NCBI UniProt Show fit	connexin 44.2
chr10_-_34002185 Show fit	3.52	ENSDART00000046599	zar1l NCBI UniProt Show fit	zygote arrest 1-like
chr2_+_6253246 Show fit	3.32	ENSDART00000058256 ENSDART00000076700	zp3b NCBI UniProt Show fit	zona pellucida glycoprotein 3b

Showing 1 to 10 of 200 entries

Network of associatons between targets according to the STRING database.

First level regulatory network of en1b_en2a+en2b_gbx1_emx1

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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
1.4	6.9	GO:0016338	calcium-independent cell-cell adhesion via plasma membrane cell-adhesion molecules(GO:0016338)
0.0	5.0	GO:0017148	negative regulation of translation(GO:0017148)
0.3	4.7	GO:0007339	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)
1.0	4.0	GO:0030718	germ-line stem cell population maintenance(GO:0030718)
0.0	3.1	GO:0008203	cholesterol metabolic process(GO:0008203)
0.2	3.0	GO:0043562	cellular response to nitrogen starvation(GO:0006995) cellular response to nitrogen levels(GO:0043562)
0.1	2.5	GO:0035469	determination of pancreatic left/right asymmetry(GO:0035469)
0.1	2.5	GO:0000038	very long-chain fatty acid metabolic process(GO:0000038)
0.1	2.3	GO:0018231	peptidyl-L-cysteine S-palmitoylation(GO:0018230) peptidyl-S-diacylglycerol-L-cysteine biosynthetic process from peptidyl-cysteine(GO:0018231)
0.1	2.2	GO:0060968	regulation of gene silencing(GO:0060968)

Showing 1 to 10 of 204 entries

Gene overrepresentation in cellular component category:

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Log-likelihood per target	Total log-likelihood	Term	Description
0.1	6.7	GO:0005923	bicellular tight junction(GO:0005923) occluding junction(GO:0070160)
0.0	6.7	GO:0031012	extracellular matrix(GO:0031012)
0.0	4.1	GO:0005730	nucleolus(GO:0005730)
0.3	3.8	GO:0034361	very-low-density lipoprotein particle(GO:0034361)
0.1	2.9	GO:0000421	autophagosome membrane(GO:0000421)
0.0	2.6	GO:0005882	intermediate filament(GO:0005882)
0.1	1.8	GO:0005682	U5 snRNP(GO:0005682)
0.6	1.7	GO:0097189	apoptotic body(GO:0097189)
0.1	1.7	GO:0005680	anaphase-promoting complex(GO:0005680)
0.1	1.5	GO:0030667	secretory granule membrane(GO:0030667)

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
2.1	10.6	GO:0009374	biotin binding(GO:0009374)
0.0	8.7	GO:0042802	identical protein binding(GO:0042802)
0.0	7.4	GO:0003729	mRNA binding(GO:0003729) poly(A) RNA binding(GO:0044822)
0.1	3.9	GO:0003727	single-stranded RNA binding(GO:0003727)
1.0	3.8	GO:0030228	lipoprotein particle receptor activity(GO:0030228)
0.3	3.3	GO:0035804	structural constituent of egg coat(GO:0035804)
0.0	2.9	GO:0031625	ubiquitin protein ligase binding(GO:0031625)
0.1	2.5	GO:0005540	hyaluronic acid binding(GO:0005540)
0.0	2.5	GO:0005178	integrin binding(GO:0005178)
0.0	2.5	GO:0042393	histone binding(GO:0042393)

Showing 1 to 10 of 130 entries

Gene overrepresentation in curated gene sets: canonical pathways category:

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Log-likelihood per target	Total log-likelihood	Term	Description
0.2	3.8	PID REELIN PATHWAY	Reelin signaling pathway
0.2	2.9	PID INTEGRIN2 PATHWAY	Beta2 integrin cell surface interactions
0.1	2.7	PID CASPASE PATHWAY	Caspase cascade in apoptosis
0.1	2.6	NABA PROTEOGLYCANS	Genes encoding proteoglycans
0.0	1.6	NABA ECM REGULATORS	Genes encoding enzymes and their regulators involved in the remodeling of the extracellular matrix
0.1	1.3	PID HIF2PATHWAY	HIF-2-alpha transcription factor network
0.0	1.1	PID MTOR 4PATHWAY	mTOR signaling pathway
0.0	1.1	PID TELOMERASE PATHWAY	Regulation of Telomerase
0.0	1.1	WNT SIGNALING	Genes related to Wnt-mediated signal transduction
0.0	1.0	ST TUMOR NECROSIS FACTOR PATHWAY	Tumor Necrosis Factor Pathway.

Showing 1 to 10 of 32 entries

Gene overrepresentation in curated gene sets: REACTOME pathways category:

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Log-likelihood per target	Total log-likelihood	Term	Description
0.2	2.8	REACTOME ASSOCIATION OF LICENSING FACTORS WITH THE PRE REPLICATIVE COMPLEX	Genes involved in Association of licensing factors with the pre-replicative complex
0.1	2.7	REACTOME APOPTOTIC CLEAVAGE OF CELLULAR PROTEINS	Genes involved in Apoptotic cleavage of cellular proteins
0.1	1.7	REACTOME CONVERSION FROM APC C CDC20 TO APC C CDH1 IN LATE ANAPHASE	Genes involved in Conversion from APC/C:Cdc20 to APC/C:Cdh1 in late anaphase
0.1	1.5	REACTOME BILE SALT AND ORGANIC ANION SLC TRANSPORTERS	Genes involved in Bile salt and organic anion SLC transporters
0.1	1.5	REACTOME GLUCONEOGENESIS	Genes involved in Gluconeogenesis
0.0	1.5	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
0.0	1.2	REACTOME COLLAGEN FORMATION	Genes involved in Collagen formation
0.2	1.1	REACTOME REGULATION OF RHEB GTPASE ACTIVITY BY AMPK	Genes involved in Regulation of Rheb GTPase activity by AMPK
0.1	1.1	REACTOME DESTABILIZATION OF MRNA BY KSRP	Genes involved in Destabilization of mRNA by KSRP
0.1	0.9	REACTOME GAMMA CARBOXYLATION TRANSPORT AND AMINO TERMINAL CLEAVAGE OF PROTEINS	Genes involved in Gamma-carboxylation, transport, and amino-terminal cleavage of proteins

Showing 1 to 10 of 42 entries

Results for en1b_en2a+en2b_gbx1_emx1

Z-value: 0.78

Motif logo

Transcription factors associated with en1b_en2a+en2b_gbx1_emx1

Activity-expression correlation:

Activity profile of en1b_en2a+en2b_gbx1_emx1 motif

Sorted Z-values of en1b_en2a+en2b_gbx1_emx1 motif

Top targets:

Network of associatons between targets according to the STRING database.

First level regulatory network of en1b_en2a+en2b_gbx1_emx1

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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: