ISMARA results: VDR+nr1i2

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PRJNA438478: RNAseq of wild type zebrafish germline

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Results for VDR+nr1i2_vdrb

Z-value: 1.18

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Transcription factors associated with VDR+nr1i2_vdrb

Gene Symbol	Gene ID	Gene Info
nr1i2 NCBI UniProt	ENSDARG00000029766	nuclear receptor subfamily 1, group I, member 2
VDR NCBI UniProt	ENSDARG00000112923	vitamin D receptor
vdrb NCBI UniProt	ENSDARG00000070721	vitamin D receptor b
vdrb NCBI UniProt	ENSDARG00000114864	vitamin D receptor b

Activity-expression correlation:

Gene	Promoter	Pearson corr. coef.	P-value	Plot
vdrb	dr11_v1_chr6_-_39005133_39005133	-0.83	1.7e-05	Click!
CABZ01088036.1	dr11_v1_chr23_+_45785563_45785563	-0.57	1.4e-02	Click!
nr1i2	dr11_v1_chr9_+_9502610_9502610	0.10	7.0e-01	Click!

Activity profile of VDR+nr1i2_vdrb motif

Sorted Z-values of VDR+nr1i2_vdrb motif

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Promoter	Log-likelihood	Transcript	Gene	Gene Info
chr5_-_42544522 Show fit	6.59	ENSDART00000157968	BX510949.1 NCBI UniProt Show fit
chr5_-_36949476 Show fit	6.04	ENSDART00000047269	h3f3c NCBI UniProt Show fit	H3 histone, family 3C
chr6_+_9893554 Show fit	5.54	ENSDART00000064979	pimr74 NCBI UniProt Show fit	Pim proto-oncogene, serine/threonine kinase, related 74
chr12_+_20506197 Show fit	5.00	ENSDART00000153010	si:zfos-754c12.2 NCBI UniProt Show fit	si:zfos-754c12.2
chr12_+_18663154 Show fit	4.62	ENSDART00000057918	si:ch211-147h1.4 NCBI UniProt Show fit	si:ch211-147h1.4
chr1_+_54626491 Show fit	4.30	ENSDART00000136063	si:ch211-202h22.9 NCBI UniProt Show fit	si:ch211-202h22.9
chr21_-_18972206 Show fit	3.73	ENSDART00000146743	pimr72 NCBI UniProt Show fit	Pim proto-oncogene, serine/threonine kinase, related 72
chr6_-_9922266 Show fit	3.71	ENSDART00000151549	pimr73 NCBI UniProt Show fit	Pim proto-oncogene, serine/threonine kinase, related 73
chr3_+_39922602 Show fit	3.37	ENSDART00000193937	cacna1ha NCBI UniProt Show fit	calcium channel, voltage-dependent, T type, alpha 1H subunit a
chr19_-_4010263 Show fit	3.30	ENSDART00000159605 ENSDART00000165541	map7d1b NCBI UniProt Show fit	MAP7 domain containing 1b

Showing 1 to 10 of 200 entries

Network of associatons between targets according to the STRING database.

First level regulatory network of VDR+nr1i2_vdrb

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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	24.4	GO:0046777	protein autophosphorylation(GO:0046777)
0.1	3.5	GO:0031532	actin cytoskeleton reorganization(GO:0031532)
0.2	3.4	GO:0086010	membrane depolarization during action potential(GO:0086010)
0.1	3.3	GO:0006636	unsaturated fatty acid biosynthetic process(GO:0006636)
0.0	2.3	GO:0008284	positive regulation of cell proliferation(GO:0008284)
0.2	2.0	GO:0032986	nucleosome disassembly(GO:0006337) chromatin disassembly(GO:0031498) protein-DNA complex disassembly(GO:0032986)
0.4	1.9	GO:0010332	response to gamma radiation(GO:0010332) cellular response to gamma radiation(GO:0071480)
0.3	1.6	GO:0010133	proline catabolic process to glutamate(GO:0010133)
0.3	1.6	GO:0044341	sodium-dependent phosphate transport(GO:0044341)
0.1	1.4	GO:0045162	clustering of voltage-gated sodium channels(GO:0045162)

Showing 1 to 10 of 61 entries

Gene overrepresentation in cellular component category:

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Log-likelihood per target	Total log-likelihood	Term	Description
0.0	4.1	GO:0005765	lysosomal membrane(GO:0005765) lytic vacuole membrane(GO:0098852)
0.1	3.4	GO:0001518	voltage-gated sodium channel complex(GO:0001518) sodium channel complex(GO:0034706)
0.0	3.3	GO:0005925	focal adhesion(GO:0005925)
0.1	2.0	GO:0016514	SWI/SNF complex(GO:0016514)
0.1	1.6	GO:0005903	brush border(GO:0005903)
0.2	1.4	GO:0070032	synaptobrevin 2-SNAP-25-syntaxin-1a-complexin I complex(GO:0070032)
0.1	1.3	GO:0070775	H3 histone acetyltransferase complex(GO:0070775) MOZ/MORF histone acetyltransferase complex(GO:0070776)
0.1	1.2	GO:0030904	retromer complex(GO:0030904)
0.0	1.0	GO:0000421	autophagosome membrane(GO:0000421)
0.0	0.9	GO:0080008	Cul4-RING E3 ubiquitin ligase complex(GO:0080008)

Showing 1 to 10 of 31 entries

Gene overrepresentation in molecular function category:

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Log-likelihood per target	Total log-likelihood	Term	Description
0.0	24.0	GO:0004674	protein serine/threonine kinase activity(GO:0004674)
0.1	5.4	GO:0005200	structural constituent of cytoskeleton(GO:0005200)
0.5	3.4	GO:0008332	low voltage-gated calcium channel activity(GO:0008332)
0.3	3.0	GO:0003691	double-stranded telomeric DNA binding(GO:0003691)
0.6	2.6	GO:0003839	gamma-glutamylcyclotransferase activity(GO:0003839)
0.0	2.0	GO:0003714	transcription corepressor activity(GO:0003714)
0.0	2.0	GO:0001228	transcriptional activator activity, RNA polymerase II transcription regulatory region sequence-specific binding(GO:0001228)
0.4	1.6	GO:0004657	proline dehydrogenase activity(GO:0004657)
0.3	1.6	GO:0005436	sodium:phosphate symporter activity(GO:0005436)
0.0	1.4	GO:0017075	syntaxin-1 binding(GO:0017075)

Showing 1 to 10 of 46 entries

Gene overrepresentation in curated gene sets: canonical pathways category:

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Log-likelihood per target	Total log-likelihood	Term	Description
0.0	1.4	PID INTEGRIN3 PATHWAY	Beta3 integrin cell surface interactions
0.1	1.0	SA CASPASE CASCADE	Apoptosis is mediated by caspases, cysteine proteases arranged in a proteolytic cascade.
0.1	0.9	SA G2 AND M PHASES	Cdc25 activates the cdc2/cyclin B complex to induce the G2/M transition.
0.0	0.6	PID MYC REPRESS PATHWAY	Validated targets of C-MYC transcriptional repression
0.0	0.5	PID GLYPICAN 1PATHWAY	Glypican 1 network
0.0	0.5	PID ILK PATHWAY	Integrin-linked kinase signaling
0.0	0.5	PID NCADHERIN PATHWAY	N-cadherin signaling events
0.0	0.4	PID FRA PATHWAY	Validated transcriptional targets of AP1 family members Fra1 and Fra2

Showing 1 to 8 of 8 entries

Gene overrepresentation in curated gene sets: REACTOME pathways category:

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Log-likelihood per target	Total log-likelihood	Term	Description
0.3	3.3	REACTOME ALPHA LINOLENIC ACID ALA METABOLISM	Genes involved in alpha-linolenic acid (ALA) metabolism
0.2	1.0	REACTOME APOPTOSIS INDUCED DNA FRAGMENTATION	Genes involved in Apoptosis induced DNA fragmentation
0.2	0.9	REACTOME RAF MAP KINASE CASCADE	Genes involved in RAF/MAP kinase cascade
0.1	0.8	REACTOME HYALURONAN UPTAKE AND DEGRADATION	Genes involved in Hyaluronan uptake and degradation
0.1	0.7	REACTOME COMMON PATHWAY	Genes involved in Common Pathway
0.1	0.6	REACTOME ADVANCED GLYCOSYLATION ENDPRODUCT RECEPTOR SIGNALING	Genes involved in Advanced glycosylation endproduct receptor signaling
0.1	0.6	REACTOME ACTIVATION OF CHAPERONE GENES BY ATF6 ALPHA	Genes involved in Activation of Chaperone Genes by ATF6-alpha
0.0	0.6	REACTOME RNA POL I TRANSCRIPTION TERMINATION	Genes involved in RNA Polymerase I Transcription Termination
0.0	0.5	REACTOME CELL EXTRACELLULAR MATRIX INTERACTIONS	Genes involved in Cell-extracellular matrix interactions
0.0	0.5	REACTOME ACTIVATION OF RAC	Genes involved in Activation of Rac

Showing 1 to 10 of 16 entries

Results for VDR+nr1i2_vdrb

Z-value: 1.18

Motif logo

Transcription factors associated with VDR+nr1i2_vdrb

Activity-expression correlation:

Activity profile of VDR+nr1i2_vdrb motif

Sorted Z-values of VDR+nr1i2_vdrb motif

Top targets:

Network of associatons between targets according to the STRING database.

First level regulatory network of VDR+nr1i2_vdrb

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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: