Identification of Breast Cancer Associated Putative Functional Single Nucleotide Polymorphisms in the Iranian Population through In Silico Analyses

Q: How can I download an article?

To download an article from SID, first log in to the site, search for the article title, and click on the 'Download Article' option.

Q: How can I download an ISI article?

To download an ISI article on SID, enter the keyword or article title in the search bar, view the relevant results, click on the desired article, and select the 'Download Article' option.

Q: How can I access the SID database?

To access the SID database, visit SID.ir, create an account, and log in to access scientific resources.

Q: Is downloading articles from SID free?

Some articles on SID are available for free, while others require payment. Details are specified on the article's page.

Nadafi Sichani Vida; Emami Seyed Alireza; BITARAF SANI MORTEZA; NASSIRI MOHAMMADREZA; Gopalan Vinod

مرکز اطلاعات علمی Scientific Information Database (SID) - Trusted Source for Research and Academic Resources

Journal Paper

Paper Information

Journal: JOURNAL OF CELL AND MOLECULAR RESEARCH Year:2020 | Volume:12 | Issue:1 Page(s): 22-32

Download Full-Text

View:

221

Download:

Cites:

Information Journal Paper

Title

Identification of Breast Cancer Associated Putative Functional Single Nucleotide Polymorphisms in the Iranian Population through In Silico Analyses

Author(s)

Keywords

Epigenetics

Functional single nucleotide polymorphisms

Genome-Wide Association Studies

Linkage Disequilibrium

RegulomeDB scoring system

Abstract

Previous studies have found several distinct alleles at both levels of transcriptional activity and protein-DNA binding manners in breast cancer patients vs. healthy individuals through multi-step experimental approaches. This study presents a computational-based model to investigate the regulatory potential and functional properties of disease-related non-coding single nucleotide polymorphisms (SNPs) variants through several online in silico tools in the Iranian population. The association between the risk of breast cancer and its putative single nucleotide polymorphisms in the Iranian population was investigated through SNPedia database and Genome-Wide Association Studies (GWAS). Furthermore, a meta-analysis was performed by Comprehensive Meta-Analysis (CMA) software. Functional analyses were carried out through LDlink, HaploReg, and RegulomeDB. The impact of each single nucleotide polymorphism on gene expression profiles and transcription factor binding sites were predicted by the RegulomeDB. "5", "6", and "1d" scores were assigned to rs3746444, rs1062577, and rs1049174 by this scoring system, respectively. RegulomeDB scores of rs3746444-MYH7B/MIR499A and rs1062577-ESR1 suggested that they are not putative Functional single nucleotide polymorphisms; and may not associate with significant eQTL signals. The “ 1d” score for rs1049174-RP11-277P12. 20 confirmed an association with the expression of the target gene. Proxy variants rs6088678 and rs2617160 have been identified using LDlink in non-coding segments. They were in strong Linkage Disequilibrium (LD) with single nucleotide polymorphisms rs3746444 and rs1049174, respectively. Also, non-coding variants rs6088678-TRPC4AP and rs2617160-RP11-277P12. 20 with high-ranked scores showed the strongest related-expression. This work provides a rapid and direct in silico-based approach for the identification of functional genetic variants in the breast cancer. These analyses were conducted to evaluate the association of intended SNPs with the regulatory elements of histones, DNases, motif changes, and selected eQTL signals. It can be extended to some other complex single nucleotide polymorphism-related diseases.

Cites

No record.

References

Cite

APA: Copy

Nadafi Sichani, Vida, Emami, Seyed Alireza, BITARAF SANI, MORTEZA, NASSIRI, MOHAMMADREZA, & Gopalan, Vinod. (2020). Identification of Breast Cancer Associated Putative Functional Single Nucleotide Polymorphisms in the Iranian Population through In Silico Analyses. JOURNAL OF CELL AND MOLECULAR RESEARCH, 12(1), 22-32. SID. https://sid.ir/paper/668389/en

Vancouver: Copy

Nadafi Sichani Vida, Emami Seyed Alireza, BITARAF SANI MORTEZA, NASSIRI MOHAMMADREZA, Gopalan Vinod. Identification of Breast Cancer Associated Putative Functional Single Nucleotide Polymorphisms in the Iranian Population through In Silico Analyses. JOURNAL OF CELL AND MOLECULAR RESEARCH[Internet]. 2020;12(1):22-32. Available from: https://sid.ir/paper/668389/en

IEEE: Copy

Vida Nadafi Sichani, Seyed Alireza Emami, MORTEZA BITARAF SANI, MOHAMMADREZA NASSIRI, and Vinod Gopalan, “Identification of Breast Cancer Associated Putative Functional Single Nucleotide Polymorphisms in the Iranian Population through In Silico Analyses,” JOURNAL OF CELL AND MOLECULAR RESEARCH, vol. 12, no. 1, pp. 22–32, 2020, [Online]. Available: https://sid.ir/paper/668389/en

Related Journal Papers

No record.

Related Seminar Papers

No record.

Related Plans

No record.

Recommended Workshops