Transcription Direction Patterns of Adjacent Genes in Mycobacterium Tuberculosis Using GENAVIS
Issue:
Volume 7, Issue 1, June 2019
Pages:
1-4
Received:
2 February 2019
Accepted:
22 March 2019
Published:
18 April 2019
Abstract: The understanding of the relationship of a gene with other genes in its neighbourhood and the implication of this relationship on the biochemical activities of the entire genome need an efficient computational tool to unfold the relationship. GENAVIS: (GENe Adjacency VIsualization Software) is an open source, platform independent web-based software for modeling neighborhood genes as binary codes. We also incorporated the feature of having an interactive visual representation of patterns of the binary code for a specific gene family in multiple microbial genomes. The concept of using binary code for representation is derived from computational thinking techniques which models problems using computer logic of applying abstraction and pattern matching to extract hidden patterns aimed at knowledge discovery. The result provides an insight into the analysis of transcriptional unit with more than one gene and genes encoding for universal stress protein, which also allows for a comparative analysis of multiple genomes as the basis for biosynthetic pathways and multi-gene function prediction.
Abstract: The understanding of the relationship of a gene with other genes in its neighbourhood and the implication of this relationship on the biochemical activities of the entire genome need an efficient computational tool to unfold the relationship. GENAVIS: (GENe Adjacency VIsualization Software) is an open source, platform independent web-based software...
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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
Issue:
Volume 7, Issue 1, June 2019
Pages:
5-10
Received:
27 June 2019
Accepted:
17 July 2019
Published:
30 July 2019
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.
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 th...
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