Biyoinformatik araçlarla VDR geni ve ürününün karşılaştırmalı analizi

Year 2007, Volume: 4 Issue: 3, 84 - 90, 01.12.2007

Lokman Varıslı Abdullah Ozgonul Osman Cen

Abstract

Amaç: Bu çalışma, insan VDR molekülüne homolog protein dizileri, promotor dizileri üzerinde genel transkripsiyon faktör bağlanma yerleri, korunan bölgelerin filogenetik ilişkileri ve araştırılan ESTdb’lerin varlığında EST verilerine bağlı ekspresyon profilleri gibi genin ve onun ürünlerinin özelliklerini araştırmak amacı ile planlandı. Gereç-Yöntem: Biz, farklı anlı türlerinde biyoinformatik araçları kullanarak ESTdb’den EST verilerine dayanarak VDR genin homolojisini, korunan bölgelerini, promotor ve ekspresyon profillerini inceledik. Sonuçlar: Bu çalışmanın sonuçları, VDR molekülünün çalışılan tüm organizmalar arasında, örneğin Macaca mulatta 98% , Saguinus oedipus 98% ve Petromyzon marinus 59% ’un insana benzediğini ve orta derecede korunduğunu gösterdi. ZnF_C4 nükleer hormon reseptöründe C4 çinko ucu ve HOLI hormonların ligand bağlama alanı alanlarına göre bir kaç benzer motif belirlendi. Ayrıca insanın normal ve kanserli dokuları arasında gen ekspresyonu bakımından anlamlı fark olduğu gösterildi. Yorum: Bu çalışma, farklı canlı türlerinde VDR gen promotoru üzerinde herhangi bir genel transkripsiyon bağlama yerinin olmadığını kanıtladı. Yakınlık metodu NJ ’na dayanarak oluşturulan filogenetik ağaçlar, ZnF_C4 ve HOLI dizilerinin yakın evrimsel ilişkisini gösterdi

Keywords

VDR, Biyoinformatik, Karşılaştırmalı genomik, in silico Biyoloji

Computational analysis of VDR gene and its product using Bioinformatics tools

Abstract

Background: The aims of this study was to analyze some properties of this gene and its products; such as the homologous protein sequences to human VDR molecule, the common transcription factor binding sites on promoter sequences, phylogenetic relationships of the conserved domains, and in silico expression profiles based on EST data that presence in ESTdb in all investigated. Methods: We investigated the homology, conserved domain, promoter and expression profiles of the VDR gene based on EST data from the ESTdb by using bioinformatics tools in different species. Results: The results of this study indicated that VDR molecule is middling conserved among all studied organisms; for example, human similar to Macaca mulatta 98% and Saguinus oedipus 98% , to Petromyzon marinus 59% . From the point of view of ZnF_C4 C4 zinc finger in nuclear hormone receptors and HOLI Ligand binding domain of hormones domains, it was obtained several similar motifs. Separately, it was seen that there was significantly difference gene expression in normal and cancer tissues of brain in human. Conclusion: This study demonstrated that there was no common transcription factor binding sites in promoter VDR gene in different species. Phylogenetic trees constructed using the neighbor-joining method NJ revealed a close evolutionary relationship of ZnF_C4 and HOLI in various species

Keywords

VDR, Bioinformatics, Comparative genomics, in silico Biology

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