Data Mining Analysis of <i>ESCO2</i> Gene Single Nucleotide Polymorphisms Associated with Roberts’s Syndrome

Sahar Mohamed Ali Mohamed Babiker; Afra Mohamed Al Bkrye; Hind Abdelaziz Elnasri; Mona Abdelrahman Mohamed Khaier

doi:doi:10.11648/j.ijgg.20200801.15

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Data Mining Analysis of ESCO2 Gene Single Nucleotide Polymorphisms Associated with Roberts’s Syndrome

Sahar Mohamed Ali Mohamed Babiker, Afra Mohamed Al Bkrye, Hind Abdelaziz Elnasri, Mona Abdelrahman Mohamed Khaier

Published in International Journal of Genetics and Genomics (Volume 8, Issue 1)

Received: 20 December 2019 Accepted: 13 January 2020 Published: 31 January 2020

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Abstract

Roberts’s syndrome is a genetic disorder characterized by limb and facial abnormalities. Affected individuals also grow slowly before and after birth. This syndrome is associated with ESCO2 (Establishment of Sister Chromatid cohesion N- acetyltransferase 2) gene mutations. SNPs in the coding region (exonal SNPs) that are non-synonymous (nsSNPs), the SNPs and related ensembles protein (ESNP) were obtained from the SNPs database (dbSNP) for computational analysis. Bioinformatics analysis of ESCO2 exonal non-synonymous SNPs initiated by GeneMANIA, SIFT, Polyphen-2, PHD, SNP&GO, Provean and ProjctHope. There were 85 nsSNPs, they had been submitted to SIFT software to predict the tolerant and intolerant SNPs, they had been sorted to 65 Tolerated SNPs and 20 Deleterious SNPs. SIFT deleterious SNPs had been tested by polyphen-2 software and the result was 3 benign SNPs, 3 possibly damaging and 14 probably damaging SNPs. The same 20 SNPs were tested using SNP&GO software and gave the same result for PHD and SNP&GO (4 diseased and 16 neutral) and the result obtained when using Provean software was 12 SNPs were neutral while only 8 SNPs were deleterious. The total nsSNPs affecting the structure, function and causing disease in the tested software were 4 nsSNPs (rs80359868, rs146312522, rs200548692, rs373708669) Protein structural analysis was done using all of CPH server, Raptor X, Project HOPE and chimera for the 4 pathological SNPs (W539, C392Y, R427C and D403V) resulted in all function prediction software. and, these results are at use for further researches and studies on this gene and it`s mutations.

Published in	International Journal of Genetics and Genomics (Volume 8, Issue 1)
DOI	10.11648/j.ijgg.20200801.15
Page(s)	41-47
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), 2020. Published by Science Publishing Group

Keywords

ESCO2 Gene, Roberts’s Syndrome, SIFT, Polyphen-2, PHD, SNP&GO and Provean

References

[1]	Miriam Gordillo, Hugo Vega, Ethylin. Wang Jabs Roberts Syndrome. Gene Reviews. April 14, 2009; Http://Www.Ncbi.Nlm.Nih.Gov/Bookslnbk1153/. Accessed 2/11/20.
[2]	Protein structure analysis of mutations causing inheritable diseases. An e-Science approach with life scientist friendly interfaces. BMC Bioinformatics. 2010 Nov 8; 11 (1): 548. DOI: 10.1186/1471-2105- 11-548. PubMed: 21059217.
[3]	Genetic Home Reference (http://ghr.nlm.nih.gov/).
[4]	Ng PC, Henikoff S. SIFT: Predicting amino acid changes that affectprotein function. Nucleic Acids Res. 2003; 31: 3812-3814.
[5]	Adzhubei I, Jordan D M, Sunyaev SR, (2013) PredictingFunctional Effect of Human Missense Mutations Using PolyPhen-2. Human Genetics. 76: 7.20.1-7.20.41.
[6]	Calabrese R, Capriotti E, Fariselli P, Martelli PL, Casadio R. (2009). Functional annotations improve the predictive score of human disease- related mutations in proteins. Human Mutation. 30; 1237-1244.
[7]	Choi, Sims GE, Murphy S, Miller JR, Chan AP (2012) Predicting the functional effect of amino acid substitutions and Indels. PLoS ONE7: e46688.
[8]	Capriotti E, Fariselli P, Casadio R. (2005) I-Mutant2.0: predicting stability changes upon mutation from the protein sequence or structure. Nucleic Acids Res., 33 (Web Server issue): W306-W310.
[9]	J. Cheng, A. Randall, and P. Baldi. Prediction of Protein Stability Changes for Single Site Mutations Using Support Vector Machines. Proteins: Structure, Function, Bioinformatics. In press, 2005.
[10]	Warde-Farley D, Donaldson SL, Comes O, Zuberi K, Badrawi R, Chao P, Franz M, Grouios C, Kazi F, Lopes CT, Maitland A, Mostafavi S, Montojo J, Shao Q, Wright G, Bader GD, Morris Q. The GeneMANIA prediction server: biological network integration for gene prioritization and predicting gene function. Nucleic Acids Res. 2010 Jul 1; 38 Suppl: W214-20
[11]	Venselaar H, Te Beek TA, Kuipers RK, Hekkelman ML, Vriend G. Protein structure analysis of mutations causing inheritable diseases. An e-Science approach with life scientist friendly interfaces. BMC Bioinformatics. 2010 Nov 8; 11: 548.
[12]	Sheng Wang, Wei Li, Shiwang Liu, and Jinbo Xu. RaptorX-property a web server for protein structure property prediction. Nucleic acids Research, 2016.
[13]	Pettersen EF, Goddard TD, Huang CC, Couch GS, Greenblatt DM, Meng EC, et al. UCSF Chimera--a visualization system for exploratory research and analysis. J Comput Chem. 2004; 25: 1605-12.
[14]	Nielsen M., Lundegaard C., Lund O., Petersen TN. CPHmodels- 3.0--remote homology modeling using structure-guided sequence profiles. Nucleic Acids Research, 2010, Vol. 38.
[15]	Van der Lelij P, Godthelp BC, Van Zon W, Van Gostaliga D, Oostra AB, etal, (2009) The cellular phenotype of Roberts syndrome fibroblasts as revealed by ectopic expression of ESCO2, PLoS ONE 4 (9): e 6936. doi: 10,1371/ Journal. pone. 0006936.

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APA Style

Sahar Mohamed Ali Mohamed Babiker, Afra Mohamed Al Bkrye, Hind Abdelaziz Elnasri, Mona Abdelrahman Mohamed Khaier. (2020). Data Mining Analysis of ESCO2 Gene Single Nucleotide Polymorphisms Associated with Roberts’s Syndrome. International Journal of Genetics and Genomics, 8(1), 41-47. https://doi.org/10.11648/j.ijgg.20200801.15

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ACS Style

Sahar Mohamed Ali Mohamed Babiker; Afra Mohamed Al Bkrye; Hind Abdelaziz Elnasri; Mona Abdelrahman Mohamed Khaier. Data Mining Analysis of ESCO2 Gene Single Nucleotide Polymorphisms Associated with Roberts’s Syndrome. Int. J. Genet. Genomics 2020, 8(1), 41-47. doi: 10.11648/j.ijgg.20200801.15

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AMA Style

Sahar Mohamed Ali Mohamed Babiker, Afra Mohamed Al Bkrye, Hind Abdelaziz Elnasri, Mona Abdelrahman Mohamed Khaier. Data Mining Analysis of ESCO2 Gene Single Nucleotide Polymorphisms Associated with Roberts’s Syndrome. Int J Genet Genomics. 2020;8(1):41-47. doi: 10.11648/j.ijgg.20200801.15

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@article{10.11648/j.ijgg.20200801.15,
  author = {Sahar Mohamed Ali Mohamed Babiker and Afra Mohamed Al Bkrye and Hind Abdelaziz Elnasri and Mona Abdelrahman Mohamed Khaier},
  title = {Data Mining Analysis of ESCO2 Gene Single Nucleotide Polymorphisms Associated with Roberts’s Syndrome},
  journal = {International Journal of Genetics and Genomics},
  volume = {8},
  number = {1},
  pages = {41-47},
  doi = {10.11648/j.ijgg.20200801.15},
  url = {https://doi.org/10.11648/j.ijgg.20200801.15},
  eprint = {https://article.sciencepublishinggroup.com/pdf/10.11648.j.ijgg.20200801.15},
  abstract = {Roberts’s syndrome is a genetic disorder characterized by limb and facial abnormalities. Affected individuals also grow slowly before and after birth. This syndrome is associated with ESCO2 (Establishment of Sister Chromatid cohesion N- acetyltransferase 2) gene mutations. SNPs in the coding region (exonal SNPs) that are non-synonymous (nsSNPs), the SNPs and related ensembles protein (ESNP) were obtained from the SNPs database (dbSNP) for computational analysis. Bioinformatics analysis of ESCO2 exonal non-synonymous SNPs initiated by GeneMANIA, SIFT, Polyphen-2, PHD, SNP&GO, Provean and ProjctHope. There were 85 nsSNPs, they had been submitted to SIFT software to predict the tolerant and intolerant SNPs, they had been sorted to 65 Tolerated SNPs and 20 Deleterious SNPs. SIFT deleterious SNPs had been tested by polyphen-2 software and the result was 3 benign SNPs, 3 possibly damaging and 14 probably damaging SNPs. The same 20 SNPs were tested using SNP&GO software and gave the same result for PHD and SNP&GO (4 diseased and 16 neutral) and the result obtained when using Provean software was 12 SNPs were neutral while only 8 SNPs were deleterious. The total nsSNPs affecting the structure, function and causing disease in the tested software were 4 nsSNPs (rs80359868, rs146312522, rs200548692, rs373708669) Protein structural analysis was done using all of CPH server, Raptor X, Project HOPE and chimera for the 4 pathological SNPs (W539, C392Y, R427C and D403V) resulted in all function prediction software. and, these results are at use for further researches and studies on this gene and it`s mutations.},
 year = {2020}
}

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TY  - JOUR
T1  - Data Mining Analysis of ESCO2 Gene Single Nucleotide Polymorphisms Associated with Roberts’s Syndrome
AU  - Sahar Mohamed Ali Mohamed Babiker
AU  - Afra Mohamed Al Bkrye
AU  - Hind Abdelaziz Elnasri
AU  - Mona Abdelrahman Mohamed Khaier
Y1  - 2020/01/31
PY  - 2020
N1  - https://doi.org/10.11648/j.ijgg.20200801.15
DO  - 10.11648/j.ijgg.20200801.15
T2  - International Journal of Genetics and Genomics
JF  - International Journal of Genetics and Genomics
JO  - International Journal of Genetics and Genomics
SP  - 41
EP  - 47
PB  - Science Publishing Group
SN  - 2376-7359
UR  - https://doi.org/10.11648/j.ijgg.20200801.15
AB  - Roberts’s syndrome is a genetic disorder characterized by limb and facial abnormalities. Affected individuals also grow slowly before and after birth. This syndrome is associated with ESCO2 (Establishment of Sister Chromatid cohesion N- acetyltransferase 2) gene mutations. SNPs in the coding region (exonal SNPs) that are non-synonymous (nsSNPs), the SNPs and related ensembles protein (ESNP) were obtained from the SNPs database (dbSNP) for computational analysis. Bioinformatics analysis of ESCO2 exonal non-synonymous SNPs initiated by GeneMANIA, SIFT, Polyphen-2, PHD, SNP&GO, Provean and ProjctHope. There were 85 nsSNPs, they had been submitted to SIFT software to predict the tolerant and intolerant SNPs, they had been sorted to 65 Tolerated SNPs and 20 Deleterious SNPs. SIFT deleterious SNPs had been tested by polyphen-2 software and the result was 3 benign SNPs, 3 possibly damaging and 14 probably damaging SNPs. The same 20 SNPs were tested using SNP&GO software and gave the same result for PHD and SNP&GO (4 diseased and 16 neutral) and the result obtained when using Provean software was 12 SNPs were neutral while only 8 SNPs were deleterious. The total nsSNPs affecting the structure, function and causing disease in the tested software were 4 nsSNPs (rs80359868, rs146312522, rs200548692, rs373708669) Protein structural analysis was done using all of CPH server, Raptor X, Project HOPE and chimera for the 4 pathological SNPs (W539, C392Y, R427C and D403V) resulted in all function prediction software. and, these results are at use for further researches and studies on this gene and it`s mutations.
VL  - 8
IS  - 1
ER  -

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Author Information

Sahar Mohamed Ali Mohamed Babiker

Department of Molecular Biology and Bioinformatics, College of Veterinary Medicine, University of Bari, Khartoum, Sudan
Afra Mohamed Al Bkrye

Department of Molecular Biology and Bioinformatics, College of Veterinary Medicine, University of Bari, Khartoum, Sudan
Hind Abdelaziz Elnasri

Department of Molecular Biology and Bioinformatics, College of Veterinary Medicine, University of Bari, Khartoum, Sudan
Mona Abdelrahman Mohamed Khaier

Department of Molecular Biology and Bioinformatics, College of Veterinary Medicine, University of Bari, Khartoum, Sudan

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APA Style

Sahar Mohamed Ali Mohamed Babiker, Afra Mohamed Al Bkrye, Hind Abdelaziz Elnasri, Mona Abdelrahman Mohamed Khaier. (2020). Data Mining Analysis of ESCO2 Gene Single Nucleotide Polymorphisms Associated with Roberts’s Syndrome. International Journal of Genetics and Genomics, 8(1), 41-47. https://doi.org/10.11648/j.ijgg.20200801.15

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ACS Style

Sahar Mohamed Ali Mohamed Babiker; Afra Mohamed Al Bkrye; Hind Abdelaziz Elnasri; Mona Abdelrahman Mohamed Khaier. Data Mining Analysis of ESCO2 Gene Single Nucleotide Polymorphisms Associated with Roberts’s Syndrome. Int. J. Genet. Genomics 2020, 8(1), 41-47. doi: 10.11648/j.ijgg.20200801.15

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AMA Style

Sahar Mohamed Ali Mohamed Babiker, Afra Mohamed Al Bkrye, Hind Abdelaziz Elnasri, Mona Abdelrahman Mohamed Khaier. Data Mining Analysis of ESCO2 Gene Single Nucleotide Polymorphisms Associated with Roberts’s Syndrome. Int J Genet Genomics. 2020;8(1):41-47. doi: 10.11648/j.ijgg.20200801.15

Copy | Download

@article{10.11648/j.ijgg.20200801.15,
  author = {Sahar Mohamed Ali Mohamed Babiker and Afra Mohamed Al Bkrye and Hind Abdelaziz Elnasri and Mona Abdelrahman Mohamed Khaier},
  title = {Data Mining Analysis of ESCO2 Gene Single Nucleotide Polymorphisms Associated with Roberts’s Syndrome},
  journal = {International Journal of Genetics and Genomics},
  volume = {8},
  number = {1},
  pages = {41-47},
  doi = {10.11648/j.ijgg.20200801.15},
  url = {https://doi.org/10.11648/j.ijgg.20200801.15},
  eprint = {https://article.sciencepublishinggroup.com/pdf/10.11648.j.ijgg.20200801.15},
  abstract = {Roberts’s syndrome is a genetic disorder characterized by limb and facial abnormalities. Affected individuals also grow slowly before and after birth. This syndrome is associated with ESCO2 (Establishment of Sister Chromatid cohesion N- acetyltransferase 2) gene mutations. SNPs in the coding region (exonal SNPs) that are non-synonymous (nsSNPs), the SNPs and related ensembles protein (ESNP) were obtained from the SNPs database (dbSNP) for computational analysis. Bioinformatics analysis of ESCO2 exonal non-synonymous SNPs initiated by GeneMANIA, SIFT, Polyphen-2, PHD, SNP&GO, Provean and ProjctHope. There were 85 nsSNPs, they had been submitted to SIFT software to predict the tolerant and intolerant SNPs, they had been sorted to 65 Tolerated SNPs and 20 Deleterious SNPs. SIFT deleterious SNPs had been tested by polyphen-2 software and the result was 3 benign SNPs, 3 possibly damaging and 14 probably damaging SNPs. The same 20 SNPs were tested using SNP&GO software and gave the same result for PHD and SNP&GO (4 diseased and 16 neutral) and the result obtained when using Provean software was 12 SNPs were neutral while only 8 SNPs were deleterious. The total nsSNPs affecting the structure, function and causing disease in the tested software were 4 nsSNPs (rs80359868, rs146312522, rs200548692, rs373708669) Protein structural analysis was done using all of CPH server, Raptor X, Project HOPE and chimera for the 4 pathological SNPs (W539, C392Y, R427C and D403V) resulted in all function prediction software. and, these results are at use for further researches and studies on this gene and it`s mutations.},
 year = {2020}
}

Copy | Download

TY  - JOUR
T1  - Data Mining Analysis of ESCO2 Gene Single Nucleotide Polymorphisms Associated with Roberts’s Syndrome
AU  - Sahar Mohamed Ali Mohamed Babiker
AU  - Afra Mohamed Al Bkrye
AU  - Hind Abdelaziz Elnasri
AU  - Mona Abdelrahman Mohamed Khaier
Y1  - 2020/01/31
PY  - 2020
N1  - https://doi.org/10.11648/j.ijgg.20200801.15
DO  - 10.11648/j.ijgg.20200801.15
T2  - International Journal of Genetics and Genomics
JF  - International Journal of Genetics and Genomics
JO  - International Journal of Genetics and Genomics
SP  - 41
EP  - 47
PB  - Science Publishing Group
SN  - 2376-7359
UR  - https://doi.org/10.11648/j.ijgg.20200801.15
AB  - Roberts’s syndrome is a genetic disorder characterized by limb and facial abnormalities. Affected individuals also grow slowly before and after birth. This syndrome is associated with ESCO2 (Establishment of Sister Chromatid cohesion N- acetyltransferase 2) gene mutations. SNPs in the coding region (exonal SNPs) that are non-synonymous (nsSNPs), the SNPs and related ensembles protein (ESNP) were obtained from the SNPs database (dbSNP) for computational analysis. Bioinformatics analysis of ESCO2 exonal non-synonymous SNPs initiated by GeneMANIA, SIFT, Polyphen-2, PHD, SNP&GO, Provean and ProjctHope. There were 85 nsSNPs, they had been submitted to SIFT software to predict the tolerant and intolerant SNPs, they had been sorted to 65 Tolerated SNPs and 20 Deleterious SNPs. SIFT deleterious SNPs had been tested by polyphen-2 software and the result was 3 benign SNPs, 3 possibly damaging and 14 probably damaging SNPs. The same 20 SNPs were tested using SNP&GO software and gave the same result for PHD and SNP&GO (4 diseased and 16 neutral) and the result obtained when using Provean software was 12 SNPs were neutral while only 8 SNPs were deleterious. The total nsSNPs affecting the structure, function and causing disease in the tested software were 4 nsSNPs (rs80359868, rs146312522, rs200548692, rs373708669) Protein structural analysis was done using all of CPH server, Raptor X, Project HOPE and chimera for the 4 pathological SNPs (W539, C392Y, R427C and D403V) resulted in all function prediction software. and, these results are at use for further researches and studies on this gene and it`s mutations.
VL  - 8
IS  - 1
ER  -

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