ISMARA results: tbr1b_tbx16+tbx16l+tbx2a+tbx2b

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PRJNA438478: RNAseq of wild type zebrafish germline

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Results for tbr1b_tbx16+tbx16l+tbx2a+tbx2b

Z-value: 2.11

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Transcription factors associated with tbr1b_tbx16+tbx16l+tbx2a+tbx2b

Gene Symbol	Gene ID	Gene Info
tbr1b NCBI UniProt	ENSDARG00000004712	T-box brain transcription factor 1b
tbx2b NCBI UniProt	ENSDARG00000006120	T-box transcription factor 2b
tbx16l NCBI UniProt	ENSDARG00000006939	T-box transcription factor 16, like
tbx16 NCBI UniProt	ENSDARG00000007329	T-box transcription factor 16
tbx2a NCBI UniProt	ENSDARG00000018025	T-box transcription factor 2a
tbx2a NCBI UniProt	ENSDARG00000109541	T-box transcription factor 2a
tbx2b NCBI UniProt	ENSDARG00000116135	T-box transcription factor 2b

Activity-expression correlation:

Gene	Promoter	Pearson corr. coef.	P-value	Plot
tbx6l	dr11_v1_chr5_+_42280372_42280372	-0.97	6.2e-11	Click!
tbx16	dr11_v1_chr8_-_51753604_51753604	-0.93	1.8e-08	Click!
tbx2b	dr11_v1_chr15_+_27364394_27364394	-0.90	2.7e-07	Click!
tbx2a	dr11_v1_chr5_-_56513825_56513825	-0.71	9.4e-04	Click!
tbr1b	dr11_v1_chr9_-_51436377_51436377	0.08	7.6e-01	Click!

Activity profile of tbr1b_tbx16+tbx16l+tbx2a+tbx2b motif

Sorted Z-values of tbr1b_tbx16+tbx16l+tbx2a+tbx2b motif

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Promoter	Log-likelihood	Transcript	Gene	Gene Info
chr13_-_51846224 Show fit	12.96	ENSDART00000184663	LT631684.2 NCBI UniProt Show fit
chr12_-_35386910 Show fit	8.62	ENSDART00000153453	camk2g1 NCBI UniProt Show fit	calcium/calmodulin-dependent protein kinase (CaM kinase) II gamma 1
chr12_-_14143344 Show fit	8.23	ENSDART00000152742	buc2l NCBI UniProt Show fit	bucky ball 2-like
chr25_+_36292057 Show fit	8.17	ENSDART00000152329	bmb NCBI UniProt Show fit	brambleberry
chr3_+_43086548 Show fit	7.76	ENSDART00000163579	si:dkey-43p13.5 NCBI UniProt Show fit	si:dkey-43p13.5
chr1_-_49521407 Show fit	7.59	ENSDART00000189845 ENSDART00000143474	zp3c NCBI UniProt Show fit	zona pellucida glycoprotein 3c
chr22_+_25681911 Show fit	6.75	ENSDART00000113381	si:dkeyp-98a7.3 NCBI UniProt Show fit	si:dkeyp-98a7.3
chr22_+_25704430 Show fit	6.64	ENSDART00000143776	si:dkeyp-98a7.3 NCBI UniProt Show fit	si:dkeyp-98a7.3
chr19_-_34999379 Show fit	6.48	ENSDART00000051751	zgc:113424 NCBI UniProt Show fit	zgc:113424
chr22_+_25715925 Show fit	6.48	ENSDART00000150650	si:dkeyp-98a7.7 NCBI UniProt Show fit	si:dkeyp-98a7.7

Showing 1 to 10 of 200 entries

Network of associatons between targets according to the STRING database.

First level regulatory network of tbr1b_tbx16+tbx16l+tbx2a+tbx2b

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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
0.5	11.1	GO:0008078	mesodermal cell migration(GO:0008078)
2.2	11.0	GO:0000741	karyogamy(GO:0000741) pronuclear fusion(GO:0007344)
0.5	9.2	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)
0.2	9.0	GO:0072114	pronephros morphogenesis(GO:0072114)
0.4	7.3	GO:0005979	regulation of glycogen biosynthetic process(GO:0005979) regulation of glucan biosynthetic process(GO:0010962)
0.2	7.1	GO:0007338	single fertilization(GO:0007338)
0.0	7.1	GO:0006511	ubiquitin-dependent protein catabolic process(GO:0006511)
0.1	6.7	GO:0048484	enteric nervous system development(GO:0048484)
2.2	6.6	GO:0090008	hypoblast development(GO:0090008)
0.1	6.1	GO:0031101	fin regeneration(GO:0031101)

Showing 1 to 10 of 306 entries

Gene overrepresentation in cellular component category:

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Log-likelihood per target	Total log-likelihood	Term	Description
0.0	15.1	GO:0005789	endoplasmic reticulum membrane(GO:0005789)
0.2	11.6	GO:0031965	nuclear membrane(GO:0031965)
0.0	10.1	GO:0005730	nucleolus(GO:0005730)
0.1	9.5	GO:0005777	peroxisome(GO:0005777) microbody(GO:0042579)
0.5	9.0	GO:0000164	protein phosphatase type 1 complex(GO:0000164)
0.4	7.2	GO:0032588	trans-Golgi network membrane(GO:0032588)
0.2	6.7	GO:0010494	cytoplasmic stress granule(GO:0010494)
0.3	4.9	GO:0030057	desmosome(GO:0030057)
0.1	4.9	GO:0019005	SCF ubiquitin ligase complex(GO:0019005)
0.0	4.8	GO:0016607	nuclear speck(GO:0016607)

Showing 1 to 10 of 125 entries

Gene overrepresentation in molecular function category:

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Log-likelihood per target	Total log-likelihood	Term	Description
0.2	50.7	GO:0030246	carbohydrate binding(GO:0030246)
0.0	11.8	GO:0003924	GTPase activity(GO:0003924)
2.6	10.5	GO:0051059	NF-kappaB binding(GO:0051059)
0.5	9.2	GO:0032190	acrosin binding(GO:0032190)
0.6	9.0	GO:2001069	glycogen binding(GO:2001069)
0.0	8.9	GO:0005085	guanyl-nucleotide exchange factor activity(GO:0005085)
0.2	8.5	GO:0004683	calmodulin-dependent protein kinase activity(GO:0004683)
0.5	8.2	GO:0002039	p53 binding(GO:0002039)
0.1	5.9	GO:0008013	beta-catenin binding(GO:0008013)
0.8	5.8	GO:0008118	N-acetyllactosaminide alpha-2,3-sialyltransferase activity(GO:0008118)

Showing 1 to 10 of 210 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	8.1	PID NETRIN PATHWAY	Netrin-mediated signaling events
0.2	6.0	PID GLYPICAN 1PATHWAY	Glypican 1 network
0.1	4.7	PID PLK1 PATHWAY	PLK1 signaling events
0.3	4.6	PID ECADHERIN KERATINOCYTE PATHWAY	E-cadherin signaling in keratinocytes
0.3	4.5	PID LPA4 PATHWAY	LPA4-mediated signaling events
0.2	4.5	ST ERK1 ERK2 MAPK PATHWAY	ERK1/ERK2 MAPK Pathway
0.1	4.3	PID BETA CATENIN NUC PATHWAY	Regulation of nuclear beta catenin signaling and target gene transcription
0.1	3.9	ST P38 MAPK PATHWAY	p38 MAPK Pathway
0.1	3.6	PID VEGFR1 2 PATHWAY	Signaling events mediated by VEGFR1 and VEGFR2
0.2	2.9	PID HEDGEHOG 2PATHWAY	Signaling events mediated by the Hedgehog family

Showing 1 to 10 of 45 entries

Gene overrepresentation in curated gene sets: REACTOME pathways category:

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Log-likelihood per target	Total log-likelihood	Term	Description
0.8	8.3	REACTOME SIGNALING BY NODAL	Genes involved in Signaling by NODAL
0.4	4.5	REACTOME ADENYLATE CYCLASE ACTIVATING PATHWAY	Genes involved in Adenylate cyclase activating pathway
0.2	4.4	REACTOME G0 AND EARLY G1	Genes involved in G0 and Early G1
0.1	4.4	REACTOME ANTIGEN ACTIVATES B CELL RECEPTOR LEADING TO GENERATION OF SECOND MESSENGERS	Genes involved in Antigen Activates B Cell Receptor Leading to Generation of Second Messengers
0.0	4.2	REACTOME ANTIGEN PROCESSING UBIQUITINATION PROTEASOME DEGRADATION	Genes involved in Antigen processing: Ubiquitination & Proteasome degradation
0.1	3.8	REACTOME NETRIN1 SIGNALING	Genes involved in Netrin-1 signaling
0.2	3.4	REACTOME MITOCHONDRIAL TRNA AMINOACYLATION	Genes involved in Mitochondrial tRNA aminoacylation
0.1	3.0	REACTOME CYTOCHROME P450 ARRANGED BY SUBSTRATE TYPE	Genes involved in Cytochrome P450 - arranged by substrate type
0.1	2.9	REACTOME ASSOCIATION OF TRIC CCT WITH TARGET PROTEINS DURING BIOSYNTHESIS	Genes involved in Association of TriC/CCT with target proteins during biosynthesis
0.1	2.6	REACTOME ADHERENS JUNCTIONS INTERACTIONS	Genes involved in Adherens junctions interactions

Showing 1 to 10 of 67 entries

Results for tbr1b_tbx16+tbx16l+tbx2a+tbx2b

Z-value: 2.11

Motif logo

Transcription factors associated with tbr1b_tbx16+tbx16l+tbx2a+tbx2b

Activity-expression correlation:

Activity profile of tbr1b_tbx16+tbx16l+tbx2a+tbx2b motif

Sorted Z-values of tbr1b_tbx16+tbx16l+tbx2a+tbx2b motif

Top targets:

Network of associatons between targets according to the STRING database.

First level regulatory network of tbr1b_tbx16+tbx16l+tbx2a+tbx2b

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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: