Prediction of Single Nucleotide Polymorphisms in TNFSF4 and Confirmation of Its Relationship with AITD and SLE: Bioinformatics Approach

Sevgi Kalkanli Tas; Eylem Cagiltay; Duygu Kirkik; Nevin Kalkanli

doi:doi:10.11648/j.cbb.20190701.12

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Prediction of Single Nucleotide Polymorphisms in TNFSF4 and Confirmation of Its Relationship with AITD and SLE: Bioinformatics Approach

Sevgi Kalkanli Tas, Eylem Cagiltay, Duygu Kirkik, Nevin Kalkanli

Published in Computational Biology and Bioinformatics (Volume 7, Issue 1)

Received: 27 June 2019 Accepted: 17 July 2019 Published: 30 July 2019

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Abstract

Tumor Necrosis Factor Ligand Superfamily Member4 (TNFSF4) has a huge family of physically homologous transmembrane proteins that regulate various functions in responding cells containing proliferation, differentiation, apoptosis, and inflammatory gene expression. TNFSF4 can play significant role in inflammatory diseases that its polymorphisms of the TNFSF4 gene are mostly related with Sjogren's syndrome, and systemic lupus erythematosus (SLE). The aim of this study is to investigate the genetic variations that may alter the expression, function and role of the TNFSF4 by using in silico methods. Single Nucleotide Polymorphisms (SNPs) on TNFSF4 are analyzed by GeneMania, SIFT, PolyPhen2, UTRscan programme, U.S. National Library of Medicine Database, ClinVar. 37 variants of TNFSF4 were found that among these 9 missense, 8 coding synonymous, 1 coding, 1 splice-3, 1 UTR-3, 11 intron, 5 UTR-5 variants. Moreover, two of them SNPs that these are rs199835957, rs372063551 were detected probably damaging by PolyPhen2 and they should be noted that vital candidates in causing diseases related to TNFSF4 and they were identified missense variants that weren’t reported in ClinVar. In the future, genes of TNFSF4, TNFSFR and CD40 may be studied on polymorphisms with experimental analysis in order to contribute to science by helping to identify disease pathogenesis.

Published in	Computational Biology and Bioinformatics (Volume 7, Issue 1)
DOI	10.11648/j.cbb.20190701.12
Page(s)	5-10
Creative Commons	This is an Open Access article, distributed under the terms of the Creative Commons Attribution 4.0 International License (http://creativecommons.org/licenses/by/4.0/), which permits unrestricted use, distribution and reproduction in any medium or format, provided the original work is properly cited.
Copyright	Copyright © The Author(s), 2024. Published by Science Publishing Group

Keywords

AITD, SLE, TNFSF4, Bioinformatics, in silico

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APA Style

Sevgi Kalkanli Tas, Eylem Cagiltay, Duygu Kirkik, Nevin Kalkanli. (2019). Prediction of Single Nucleotide Polymorphisms in TNFSF4 and Confirmation of Its Relationship with AITD and SLE: Bioinformatics Approach. Computational Biology and Bioinformatics, 7(1), 5-10. https://doi.org/10.11648/j.cbb.20190701.12

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ACS Style

Sevgi Kalkanli Tas; Eylem Cagiltay; Duygu Kirkik; Nevin Kalkanli. Prediction of Single Nucleotide Polymorphisms in TNFSF4 and Confirmation of Its Relationship with AITD and SLE: Bioinformatics Approach. Comput. Biol. Bioinform. 2019, 7(1), 5-10. doi: 10.11648/j.cbb.20190701.12

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AMA Style

Sevgi Kalkanli Tas, Eylem Cagiltay, Duygu Kirkik, Nevin Kalkanli. Prediction of Single Nucleotide Polymorphisms in TNFSF4 and Confirmation of Its Relationship with AITD and SLE: Bioinformatics Approach. Comput Biol Bioinform. 2019;7(1):5-10. doi: 10.11648/j.cbb.20190701.12

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@article{10.11648/j.cbb.20190701.12,
  author = {Sevgi Kalkanli Tas and Eylem Cagiltay and Duygu Kirkik and Nevin Kalkanli},
  title = {Prediction of Single Nucleotide Polymorphisms in TNFSF4 and Confirmation of Its Relationship with AITD and SLE: Bioinformatics Approach},
  journal = {Computational Biology and Bioinformatics},
  volume = {7},
  number = {1},
  pages = {5-10},
  doi = {10.11648/j.cbb.20190701.12},
  url = {https://doi.org/10.11648/j.cbb.20190701.12},
  eprint = {https://article.sciencepublishinggroup.com/pdf/10.11648.j.cbb.20190701.12},
  abstract = {Tumor Necrosis Factor Ligand Superfamily Member4 (TNFSF4) has a huge family of physically homologous transmembrane proteins that regulate various functions in responding cells containing proliferation, differentiation, apoptosis, and inflammatory gene expression. TNFSF4 can play significant role in inflammatory diseases that its polymorphisms of the TNFSF4 gene are mostly related with Sjogren's syndrome, and systemic lupus erythematosus (SLE). The aim of this study is to investigate the genetic variations that may alter the expression, function and role of the TNFSF4 by using in silico methods. Single Nucleotide Polymorphisms (SNPs) on TNFSF4 are analyzed by GeneMania, SIFT, PolyPhen2, UTRscan programme, U.S. National Library of Medicine Database, ClinVar. 37 variants of TNFSF4 were found that among these 9 missense, 8 coding synonymous, 1 coding, 1 splice-3, 1 UTR-3, 11 intron, 5 UTR-5 variants. Moreover, two of them SNPs that these are rs199835957, rs372063551 were detected probably damaging by PolyPhen2 and they should be noted that vital candidates in causing diseases related to TNFSF4 and they were identified missense variants that weren’t reported in ClinVar. In the future, genes of TNFSF4, TNFSFR and CD40 may be studied on polymorphisms with experimental analysis in order to contribute to science by helping to identify disease pathogenesis.},
 year = {2019}
}

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TY  - JOUR
T1  - Prediction of Single Nucleotide Polymorphisms in TNFSF4 and Confirmation of Its Relationship with AITD and SLE: Bioinformatics Approach
AU  - Sevgi Kalkanli Tas
AU  - Eylem Cagiltay
AU  - Duygu Kirkik
AU  - Nevin Kalkanli
Y1  - 2019/07/30
PY  - 2019
N1  - https://doi.org/10.11648/j.cbb.20190701.12
DO  - 10.11648/j.cbb.20190701.12
T2  - Computational Biology and Bioinformatics
JF  - Computational Biology and Bioinformatics
JO  - Computational Biology and Bioinformatics
SP  - 5
EP  - 10
PB  - Science Publishing Group
SN  - 2330-8281
UR  - https://doi.org/10.11648/j.cbb.20190701.12
AB  - Tumor Necrosis Factor Ligand Superfamily Member4 (TNFSF4) has a huge family of physically homologous transmembrane proteins that regulate various functions in responding cells containing proliferation, differentiation, apoptosis, and inflammatory gene expression. TNFSF4 can play significant role in inflammatory diseases that its polymorphisms of the TNFSF4 gene are mostly related with Sjogren's syndrome, and systemic lupus erythematosus (SLE). The aim of this study is to investigate the genetic variations that may alter the expression, function and role of the TNFSF4 by using in silico methods. Single Nucleotide Polymorphisms (SNPs) on TNFSF4 are analyzed by GeneMania, SIFT, PolyPhen2, UTRscan programme, U.S. National Library of Medicine Database, ClinVar. 37 variants of TNFSF4 were found that among these 9 missense, 8 coding synonymous, 1 coding, 1 splice-3, 1 UTR-3, 11 intron, 5 UTR-5 variants. Moreover, two of them SNPs that these are rs199835957, rs372063551 were detected probably damaging by PolyPhen2 and they should be noted that vital candidates in causing diseases related to TNFSF4 and they were identified missense variants that weren’t reported in ClinVar. In the future, genes of TNFSF4, TNFSFR and CD40 may be studied on polymorphisms with experimental analysis in order to contribute to science by helping to identify disease pathogenesis.
VL  - 7
IS  - 1
ER  -

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Author Information

Sevgi Kalkanli Tas

Department of Immunology, Faculty of Medicine, University of Health Sciences, Istanbul, Turkey
Eylem Cagiltay

Department of Endocrinology, Sultan Abdulhamid Han Training & Research Hospital, Istanbul, Turkey
Duygu Kirkik

Department of Medical Biology, Faculty of Medicine, University of Health Sciences, Istanbul Turkey
Nevin Kalkanli

Department of Dermatology, Ozel Diyarlife Hospital, Diyarbakir, Turkey

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APA Style

Sevgi Kalkanli Tas, Eylem Cagiltay, Duygu Kirkik, Nevin Kalkanli. (2019). Prediction of Single Nucleotide Polymorphisms in TNFSF4 and Confirmation of Its Relationship with AITD and SLE: Bioinformatics Approach. Computational Biology and Bioinformatics, 7(1), 5-10. https://doi.org/10.11648/j.cbb.20190701.12

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ACS Style

Sevgi Kalkanli Tas; Eylem Cagiltay; Duygu Kirkik; Nevin Kalkanli. Prediction of Single Nucleotide Polymorphisms in TNFSF4 and Confirmation of Its Relationship with AITD and SLE: Bioinformatics Approach. Comput. Biol. Bioinform. 2019, 7(1), 5-10. doi: 10.11648/j.cbb.20190701.12

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AMA Style

Sevgi Kalkanli Tas, Eylem Cagiltay, Duygu Kirkik, Nevin Kalkanli. Prediction of Single Nucleotide Polymorphisms in TNFSF4 and Confirmation of Its Relationship with AITD and SLE: Bioinformatics Approach. Comput Biol Bioinform. 2019;7(1):5-10. doi: 10.11648/j.cbb.20190701.12

Copy | Download

@article{10.11648/j.cbb.20190701.12,
  author = {Sevgi Kalkanli Tas and Eylem Cagiltay and Duygu Kirkik and Nevin Kalkanli},
  title = {Prediction of Single Nucleotide Polymorphisms in TNFSF4 and Confirmation of Its Relationship with AITD and SLE: Bioinformatics Approach},
  journal = {Computational Biology and Bioinformatics},
  volume = {7},
  number = {1},
  pages = {5-10},
  doi = {10.11648/j.cbb.20190701.12},
  url = {https://doi.org/10.11648/j.cbb.20190701.12},
  eprint = {https://article.sciencepublishinggroup.com/pdf/10.11648.j.cbb.20190701.12},
  abstract = {Tumor Necrosis Factor Ligand Superfamily Member4 (TNFSF4) has a huge family of physically homologous transmembrane proteins that regulate various functions in responding cells containing proliferation, differentiation, apoptosis, and inflammatory gene expression. TNFSF4 can play significant role in inflammatory diseases that its polymorphisms of the TNFSF4 gene are mostly related with Sjogren's syndrome, and systemic lupus erythematosus (SLE). The aim of this study is to investigate the genetic variations that may alter the expression, function and role of the TNFSF4 by using in silico methods. Single Nucleotide Polymorphisms (SNPs) on TNFSF4 are analyzed by GeneMania, SIFT, PolyPhen2, UTRscan programme, U.S. National Library of Medicine Database, ClinVar. 37 variants of TNFSF4 were found that among these 9 missense, 8 coding synonymous, 1 coding, 1 splice-3, 1 UTR-3, 11 intron, 5 UTR-5 variants. Moreover, two of them SNPs that these are rs199835957, rs372063551 were detected probably damaging by PolyPhen2 and they should be noted that vital candidates in causing diseases related to TNFSF4 and they were identified missense variants that weren’t reported in ClinVar. In the future, genes of TNFSF4, TNFSFR and CD40 may be studied on polymorphisms with experimental analysis in order to contribute to science by helping to identify disease pathogenesis.},
 year = {2019}
}

Copy | Download

TY  - JOUR
T1  - Prediction of Single Nucleotide Polymorphisms in TNFSF4 and Confirmation of Its Relationship with AITD and SLE: Bioinformatics Approach
AU  - Sevgi Kalkanli Tas
AU  - Eylem Cagiltay
AU  - Duygu Kirkik
AU  - Nevin Kalkanli
Y1  - 2019/07/30
PY  - 2019
N1  - https://doi.org/10.11648/j.cbb.20190701.12
DO  - 10.11648/j.cbb.20190701.12
T2  - Computational Biology and Bioinformatics
JF  - Computational Biology and Bioinformatics
JO  - Computational Biology and Bioinformatics
SP  - 5
EP  - 10
PB  - Science Publishing Group
SN  - 2330-8281
UR  - https://doi.org/10.11648/j.cbb.20190701.12
AB  - Tumor Necrosis Factor Ligand Superfamily Member4 (TNFSF4) has a huge family of physically homologous transmembrane proteins that regulate various functions in responding cells containing proliferation, differentiation, apoptosis, and inflammatory gene expression. TNFSF4 can play significant role in inflammatory diseases that its polymorphisms of the TNFSF4 gene are mostly related with Sjogren's syndrome, and systemic lupus erythematosus (SLE). The aim of this study is to investigate the genetic variations that may alter the expression, function and role of the TNFSF4 by using in silico methods. Single Nucleotide Polymorphisms (SNPs) on TNFSF4 are analyzed by GeneMania, SIFT, PolyPhen2, UTRscan programme, U.S. National Library of Medicine Database, ClinVar. 37 variants of TNFSF4 were found that among these 9 missense, 8 coding synonymous, 1 coding, 1 splice-3, 1 UTR-3, 11 intron, 5 UTR-5 variants. Moreover, two of them SNPs that these are rs199835957, rs372063551 were detected probably damaging by PolyPhen2 and they should be noted that vital candidates in causing diseases related to TNFSF4 and they were identified missense variants that weren’t reported in ClinVar. In the future, genes of TNFSF4, TNFSFR and CD40 may be studied on polymorphisms with experimental analysis in order to contribute to science by helping to identify disease pathogenesis.
VL  - 7
IS  - 1
ER  -

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