TISIDB

Summary
Symbol	SETX
Name	senataxin
Aliases	KIAA0625; AOA2; ALS4; amyotrophic lateral sclerosis 4; spinocerebellar ataxia, recessive, non-Friedreich typ ......
Chromosomal Location	9q34
External Links	HGNC, NCBI, Ensembl, Uniprot, GeneCards
Content	Basic function annotation. > Subcellular Location, Domain and Function > Gene Ontology > KEGG and Reactome Pathway

> Subcellular Location, Domain and Function [ TOP ]
Subcellular Location	Nucleus Nucleus, nucleoplasm Nucleus, nucleolus Cytoplasm Chromosome Chromosome, telomere Cell projection, axon Cell projection, growth cone Note=May be detected in the nucleolus only in cycling cells. At pachytene stage, colocalizes predominantly to the heterochromatic XY-body of sex chromosomes with DNA damage response proteins in a BRCA1-dependent manner (By similarity). Localizes with telomeric DNA in a transcription-dependent manner (PubMed:21112256). Under replication stress, colocalizes with a variety of DNA damage signaling and repair response proteins at distinct nuclear foci in mitotic S/G2- and G1-phase cells in a transcription- and RNA/DNA hybrid-dependent manner (PubMed:23149945). Localizes at limited number of nuclear foci (PubMed:24105744). Colocalizes with EXOSC9 in nuclear foci upon induction of transcription-related DNA damage at the S phase (PubMed:24105744). Most abundant in the nucleus. Detected in granules. Colocalized in cycling cells with FBL in the nucleolus.
Domain	-
Function	Probable RNA/DNA helicase involved in diverse aspects of RNA metabolism and genomic integrity. Plays a role in transcription regulation by its ability to modulate RNA Polymerase II (Pol II) binding to chromatin and through its interaction with proteins involved in transcription (PubMed:19515850, PubMed:21700224). Contributes to the mRNA splicing efficiency and splice site selection (PubMed:19515850). Required for the resolution of R-loop RNA-DNA hybrid formation at G-rich pause sites located downstream of the poly(A) site, allowing XRN2 recruitment and XRN2-mediated degradation of the downstream cleaved RNA and hence efficient RNA polymerase II (RNAp II) transcription termination (PubMed:19515850, PubMed:21700224, PubMed:26700805). Required for the 3' transcriptional termination of PER1 and CRY2, thus playing an important role in the circadian rhythm regulation (By similarity). Involved in DNA double-strand breaks damage response generated by oxidative stress (PubMed:17562789). In association with RRP45, targets the RNA exosome complex to sites of transcription-induced DNA damage (PubMed:24105744). Plays a role in the development and maturation of germ cells: essential for male meiosis, acting at the interface of transcription and meiotic recombination, and in the process of gene silencing during meiotic sex chromosome inactivation (MSCI) (By similarity). May be involved in telomeric stability through the regulation of telomere repeat-containing RNA (TERRA) transcription (PubMed:21112256). Plays a role in neurite outgrowth in hippocampal cells through FGF8-activated signaling pathways. Inhibits retinoic acid-induced apoptosis (PubMed:21576111).

> Gene Ontology [ TOP ]
Biological Process	GO:0000245 spliceosomal complex assembly GO:0000302 response to reactive oxygen species GO:0000375 RNA splicing, via transesterification reactions GO:0000377 RNA splicing, via transesterification reactions with bulged adenosine as nucleophile GO:0000398 mRNA splicing, via spliceosome GO:0001101 response to acid chemical GO:0006302 double-strand break repair GO:0006310 DNA recombination GO:0006352 DNA-templated transcription, initiation GO:0006353 DNA-templated transcription, termination GO:0006369 termination of RNA polymerase II transcription GO:0006376 mRNA splice site selection GO:0006397 mRNA processing GO:0006979 response to oxidative stress GO:0007283 spermatogenesis GO:0007623 circadian rhythm GO:0008380 RNA splicing GO:0008543 fibroblast growth factor receptor signaling pathway GO:0010035 response to inorganic substance GO:0010720 positive regulation of cell development GO:0010975 regulation of neuron projection development GO:0010976 positive regulation of neuron projection development GO:0022613 ribonucleoprotein complex biogenesis GO:0022618 ribonucleoprotein complex assembly GO:0030846 termination of RNA polymerase II transcription, poly(A)-coupled GO:0031334 positive regulation of protein complex assembly GO:0031346 positive regulation of cell projection organization GO:0031554 regulation of DNA-templated transcription, termination GO:0032392 DNA geometric change GO:0032508 DNA duplex unwinding GO:0032526 response to retinoic acid GO:0032984 macromolecular complex disassembly GO:0033120 positive regulation of RNA splicing GO:0034599 cellular response to oxidative stress GO:0034614 cellular response to reactive oxygen species GO:0042542 response to hydrogen peroxide GO:0043241 protein complex disassembly GO:0043243 positive regulation of protein complex disassembly GO:0043244 regulation of protein complex disassembly GO:0043254 regulation of protein complex assembly GO:0043484 regulation of RNA splicing GO:0043491 protein kinase B signaling GO:0044089 positive regulation of cellular component biogenesis GO:0044344 cellular response to fibroblast growth factor stimulus GO:0045666 positive regulation of neuron differentiation GO:0048232 male gamete generation GO:0048511 rhythmic process GO:0050769 positive regulation of neurogenesis GO:0051962 positive regulation of nervous system development GO:0060566 positive regulation of DNA-templated transcription, termination GO:0070301 cellular response to hydrogen peroxide GO:0071103 DNA conformation change GO:0071229 cellular response to acid chemical GO:0071300 cellular response to retinoic acid GO:0071396 cellular response to lipid GO:0071774 response to fibroblast growth factor GO:0071826 ribonucleoprotein complex subunit organization GO:1904594 regulation of termination of RNA polymerase II transcription GO:1904595 positive regulation of termination of RNA polymerase II transcription GO:2000142 regulation of DNA-templated transcription, initiation GO:2000144 positive regulation of DNA-templated transcription, initiation GO:2000804 regulation of termination of RNA polymerase II transcription, poly(A)-coupled GO:2000806 positive regulation of termination of RNA polymerase II transcription, poly(A)-coupled
Molecular Function	GO:0001147 transcription termination site sequence-specific DNA binding GO:0001160 transcription termination site DNA binding GO:0003678 DNA helicase activity GO:0004386 helicase activity
Cellular Component	GO:0000781 chromosome, telomeric region GO:0030424 axon GO:0030426 growth cone GO:0030427 site of polarized growth GO:0098687 chromosomal region

> KEGG and Reactome Pathway [ TOP ]
KEGG	-
Reactome	-

Summary
Symbol	SETX
Name	senataxin
Aliases	KIAA0625; AOA2; ALS4; amyotrophic lateral sclerosis 4; spinocerebellar ataxia, recessive, non-Friedreich typ ......
Chromosomal Location	9q34
External Links	HGNC, NCBI, Ensembl, Uniprot, GeneCards
Content	Literatures that report relations between SETX and anti-tumor immunity. The specific mechanism were also collected if the literature reports that a gene specifically promotes or inhibits the infiltration or function of T/NK cells.

> Text Mining [ TOP ]
There is no record.

Summary
Symbol	SETX
Name	senataxin
Aliases	KIAA0625; AOA2; ALS4; amyotrophic lateral sclerosis 4; spinocerebellar ataxia, recessive, non-Friedreich typ ......
Chromosomal Location	9q34
External Links	HGNC, NCBI, Ensembl, Uniprot, GeneCards
Content	High-throughput screening data (e.g. CRISPR-Cas9, shRNA and RNAi) for T cell-mediated killing. Genetic screen techniques can identify mechanisms of tumor cell resistance (e.g., PTPN2) and sensitivity (e.g., APLNR) to killing by cytotoxic T cells, the central effectors of anti-tumor immunity. After comprehensively searching, eight groups of screening data sets were collected in the current database. In this tab, users can check whether their selected genes cause resistance or increase sensitivity to T cell-mediated killing in various data sets.

> High-throughput Screening

[ TOP ]

Statistical results of SETX in screening data sets for detecting immune reponses.

PMID	Screening System	Cancer Type	Cell Line	Data Set	Statistical Results	Relation to immunity
29301958	CRISPR-Cas9	melanoma	B16F10	Pmel-1 T cell	NA/NS	NA/NS
29301958	CRISPR-Cas9	melanoma	B16F10	OT-1 T cell	NA/NS	NA/NS
28783722	CRISPR-Cas9	melanoma	Mel624	2CT-CRISPR	NA/NS	NA/NS
28723893	CRISPR-Cas9	melanoma	B16	GVAX+Anti-PD1	NA/NS	NA/NS
28723893	CRISPR-Cas9	melanoma	B16	GVAX	NA/NS	NA/NS
25691366	RNAi	Breast cancer	MCF7	Luc-CTL assay	NA/NS	NA/NS
24476824	shRNA	melanoma	B16	Primary screen	NA/NS	NA/NS
24476824	shRNA	melanoma	B16	Secondary screen	NA/NS	NA/NS

Summary
Symbol	SETX
Name	senataxin
Aliases	KIAA0625; AOA2; ALS4; amyotrophic lateral sclerosis 4; spinocerebellar ataxia, recessive, non-Friedreich typ ......
Chromosomal Location	9q34
External Links	HGNC, NCBI, Ensembl, Uniprot, GeneCards
Content	Transcriptomic and genomic profiling of pre-treated tumor biopsies from responders and non-responders to immunotherapy. These data were used to identify signatures and mechanisms of response to checkpoint blockade (e.g., anti-PDL1 and anti-PD1). One example is that mutations in the gene PBRM1 benefit clinical survival of patients with clear cell renal cell carcinoma. After comprehensively searching, we collected 5 and 6 of transcriptomic and genomic data sets, respectively. In this tab, users can check whether their selected genes have significant difference of expression or mutation between responders and non-responders in various data sets. > Expression difference between responders and non-responders > Mutation difference between responders and non-responders

> Expression difference between responders and non-responders

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Points in the above scatter plot represent the expression difference of SETX in various data sets.

No	PMID	Cancer type	Group	Drug	# Res	# NRes	Log2 (Fold Change)	P value
1	26997480	Melanoma	all	Anti-PD-1 (pembrolizumab and nivolumab)	14	12	0.018	0.948
2	26997480	Melanoma	MAPKi	Anti-PD-1 (pembrolizumab and nivolumab)	6	5	0.292	0.836
3	26997480	Melanoma	non-MAPKi	Anti-PD-1 (pembrolizumab and nivolumab)	8	7	-0.184	0.865
4	28552987	Urothelial cancer	all	Anti-PD-L1 (atezolizumab)	9	16	0.092	0.796
5	28552987	Urothelial cancer	smoking	Anti-PD-L1 (atezolizumab)	5	9	-0.304	0.91
6	28552987	Urothelial cancer	non-smoking	Anti-PD-L1 (atezolizumab)	4	7	0.599	0.869
7	29033130	Melanoma	all	Anti-PD-1 (nivolumab)	26	23	0.405	0.329
8	29033130	Melanoma	NIV3-PROG	Anti-PD-1 (nivolumab)	15	11	0.418	0.827
9	29033130	Melanoma	NIV3-NAIVE	Anti-PD-1 (nivolumab)	11	12	0.413	0.845
10	29301960	Clear cell renal cell carcinoma (ccRCC)	all	Anti-PD-1 (nivolumab)	4	8	0.884	0.515
11	29301960	Clear cell renal cell carcinoma (ccRCC)	VEGFRi	Anti-PD-1 (nivolumab)	2	0	0	1
12	29301960	Clear cell renal cell carcinoma (ccRCC)	non-VEGFRi	Anti-PD-1 (nivolumab)	2	8	1.309	0.513
13	29443960	Urothelial cancer	all	Anti-PD-L1 (atezolizumab)	68	230	-0.046	0.438

> Mutation difference between responders and non-responders

[ TOP ]

Points in the above scatter plot represent the mutation difference of SETX in various data sets.

No	PMID	Cancer type	Group	Drug	# Res	# NRes	% Mut/Res	% Mut/NRes	% Diff (R vs NR)	Pval
1	25765070	Non-small cell lung cancer (NSCLC)	all	Anti-PD-1 (pembrolizumab)	14	17	0	5.9	-5.9	1
2	25765070	Non-small cell lung cancer (NSCLC)	smoking	Anti-PD-1 (pembrolizumab)	10	3	0	0	0	1
3	25765070	Non-small cell lung cancer (NSCLC)	non-smoking	Anti-PD-1 (pembrolizumab)	4	14	0	7.1	-7.1	1
4	26359337	Melanoma	all	Anti-CTLA-4 (ipilimumab)	27	73	18.5	4.1	14.4	0.0315
5	26359337	Melanoma	BRAFi	Anti-CTLA-4 (ipilimumab)	0	14	0	0	0	1
6	26359337	Melanoma	non-BRAFi	Anti-CTLA-4 (ipilimumab)	27	59	18.5	5.1	13.4	0.102
7	26997480	Melanoma	all	Anti-PD-1 (pembrolizumab and nivolumab)	21	17	9.5	0	9.5	0.492
8	26997480	Melanoma	MAPKi	Anti-PD-1 (pembrolizumab and nivolumab)	8	6	12.5	0	12.5	1
9	26997480	Melanoma	non-MAPKi	Anti-PD-1 (pembrolizumab and nivolumab)	13	11	7.7	0	7.7	1
10	28552987	Urothelial cancer	all	Anti-PD-L1 (atezolizumab)	9	16	11.1	0	11.1	0.36
11	28552987	Urothelial cancer	smoking	Anti-PD-L1 (atezolizumab)	5	9	0	0	0	1
12	28552987	Urothelial cancer	non-smoking	Anti-PD-L1 (atezolizumab)	4	7	25	0	25	0.364
13	29033130	Melanoma	all	Anti-PD-1 (nivolumab)	38	27	0	0	0	1
14	29033130	Melanoma	NIV3-PROG	Anti-PD-1 (nivolumab)	22	13	0	0	0	1
15	29033130	Melanoma	NIV3-NAIVE	Anti-PD-1 (nivolumab)	16	14	0	0	0	1
16	29301960	Clear cell renal cell carcinoma (ccRCC)	all	Anti-PD-1 (nivolumab)	11	13	0	0	0	1
17	29301960	Clear cell renal cell carcinoma (ccRCC)	VEGFRi	Anti-PD-1 (nivolumab)	6	1	0	0	0	1
18	29301960	Clear cell renal cell carcinoma (ccRCC)	non-VEGFRi	Anti-PD-1 (nivolumab)	5	12	0	0	0	1

Summary
Symbol	SETX
Name	senataxin
Aliases	KIAA0625; AOA2; ALS4; amyotrophic lateral sclerosis 4; spinocerebellar ataxia, recessive, non-Friedreich typ ......
Chromosomal Location	9q34
External Links	HGNC, NCBI, Ensembl, Uniprot, GeneCards
Content	Relations between abundance of tumor-infiltrating lymphocytes (TILs) and expression, copy number, methylation, or mutation of SETX. The immune-related signatures of 28 TIL types from Charoentong's study, which can be viewed in the download page. For each cancer type, the relative abundance of TILs were inferred by using gene set variation analysis (GSVA) based on gene expression profile. In this tab, users can examine which kinds of TILs might be regulated by the current gene.

> Lymphocyte [ TOP ]

Summary
Symbol	SETX
Name	senataxin
Aliases	KIAA0625; AOA2; ALS4; amyotrophic lateral sclerosis 4; spinocerebellar ataxia, recessive, non-Friedreich typ ......
Chromosomal Location	9q34
External Links	HGNC, NCBI, Ensembl, Uniprot, GeneCards
Content	Relations between three kinds of immunomodulators and expression, copy number, methylation, or mutation of SETX. These immunomo-dulators were collected from Charoentong's study. In this tab, users can examine which immunomodulators might be regulated by SETX. > Immunoinhibitor > Immunostimulator > MHC molecule

> Immunoinhibitor [ TOP ]

> Immunostimulator [ TOP ]

> MHC molecule [ TOP ]

Summary
Symbol	SETX
Name	senataxin
Aliases	KIAA0625; AOA2; ALS4; amyotrophic lateral sclerosis 4; spinocerebellar ataxia, recessive, non-Friedreich typ ......
Chromosomal Location	9q34
External Links	HGNC, NCBI, Ensembl, Uniprot, GeneCards
Content	Relations between chemokines (or receptors) and expression, copy number, methylation, or mutation of SETX. In this tab, users can examine which chemokines (or receptors) might be regulated by the current gene. > Chemokine > Receptor

> Chemokine [ TOP ]

> Receptor [ TOP ]

Summary
Symbol	SETX
Name	senataxin
Aliases	KIAA0625; AOA2; ALS4; amyotrophic lateral sclerosis 4; spinocerebellar ataxia, recessive, non-Friedreich typ ......
Chromosomal Location	9q34
External Links	HGNC, NCBI, Ensembl, Uniprot, GeneCards
Content	Distribution of SETX expression across immune and molecular subtypes. > Immune subtype > Molecular subtype

> Immune subtype [ TOP ]

> Molecular subtype [ TOP ]

Summary
Symbol	SETX
Name	senataxin
Aliases	KIAA0625; AOA2; ALS4; amyotrophic lateral sclerosis 4; spinocerebellar ataxia, recessive, non-Friedreich typ ......
Chromosomal Location	9q34
External Links	HGNC, NCBI, Ensembl, Uniprot, GeneCards
Content	Associations between SETX and clinical features. > Overall survival analysis > Cancer stage > Tumor grade

> Overall survival [ TOP ]

> Stage [ TOP ]

> Grade [ TOP ]

Summary
Symbol	SETX
Name	senataxin
Aliases	KIAA0625; AOA2; ALS4; amyotrophic lateral sclerosis 4; spinocerebellar ataxia, recessive, non-Friedreich typ ......
Chromosomal Location	9q34
External Links	HGNC, NCBI, Ensembl, Uniprot, GeneCards
Content	Drugs targeting SETX collected from DrugBank database.

> Drugs from DrugBank database [ TOP ]
There is no record.

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