Protein – Protein Etkileşimi Tespit Yöntemleri, Veri Tabanları ve Veri Güvenilirliği

Year 2020, Issue: 19, 722 - 733, 31.08.2020

Volkan Altuntaş , Murat Gök

https://doi.org/10.31590/ejosat.724390

Cited By: 2

Abstract

Önemli biyolojik aktiviteler tek bir molekülün sonucu değil, birbirleriyle etkileşime giren çoklu moleküllerin etkilerinin ürünü olarak
ortaya çıkmaktadır. Protein-protein etkileşimlerinin belirlenmesi, ilgili proteinlere ait fonksiyonların tespit edilmesi için önemli bilgi
sağlamaktadır. Genlerin ve proteinlerin büyük bir çoğunluğu işlevlerini birbirleriyle etkileşimleri sonucunda oluşturmaktadırlar.
Protein-protein etkileşimlerini incelemek için çok sayıda yöntem geliştirilmiştir. Etkileşimlerin tespitinde in vitro, in vivo ve in siliko
olarak adlandırılan 3 temel yaklaşım bulunmaktadır. In vitro ve in vivo yöntemlerin maliyet, zaman gibi sınırlamaları bulunur. İn
siliko yöntemler deneysel yönlendirme ile maliyet ve zaman kazancı için geliştirilmiştir. Yöntemler sonucunda oluşan veri setleri
gürültülüdür, çok sayıda yanlış pozitif ve yanlış negatif değerler içermektedirler. Protein etkileşim tespit yöntemlerindeki gelişmeler
hastalıkların tespit edilmesi, model organizmalara ait yolakların ve protein komplekslerinin belirlenmesi gibi birçok alana doğrudan
etki etmektedir. Yapılan çalışmalar sonucunda tespit edilen etkileşimler veri tabanlarında saklanmakta ve ücretsiz olarak
erişilebilmektedir. Metotların hızlanması ile tespit edilen etkileşim sayısındaki artış, elde edilen bu verilerin analiz edilmesini, bir veya
birden fazla metot ile sağlanmasını ve doğruluğunun belirlenmesini önemli hale getirmektedir. Bu çalışmada protein-protein etkileşim
tespitinde kullanılan in vitro, in vivo ve in siliko yöntemler ve protein-protein etkileşim veri tabanları incelenmektedir. Tespit
yöntemlerinin artıları ve eksileri araştırılmış ve yöntemlerin avantaj ve dezavantajları paylaşılmıştır. Veri tabanlarının içerdiği bilgiler
karşılaştırılmış, benzerlik oranları ve sebepleri araştırılmıştır.

Keywords

Protein, Protein-protein etkileşimi, PPI tespit yöntemleri, PPI veri tabanları

Protein - Protein Interaction Detection Methods, Databases and Data Reliability

Abstract

Important biological activities do not result from a single molecule but as a result of the effects of multiple molecules interacting with each other. The determination of protein-protein interactions provides important information for determining the functions of the respective proteins. The most majority of genes and proteins function as a result of interactions with each other. Numerous methods have been developed to study protein-protein interactions. In the determination of interactions, there are three basic approaches called in vitro, in vivo, and in silico. In vitro and in vivo methods have limitations such as cost and time. In silico methods have been developed for cost and time savings with experimental guidance. The data sets generated by the methods are noisy and contain a large number of false-positive and false-negative values. Advances in protein interaction detection methods have a direct impact on many areas such as the detection of diseases, pathways of model organisms, and protein complexes. The interactions identified as a result of the studies are stored in the databases and can be accessed free of charge. With the increase in the number of interactions detected by accelerated methods, it became important to analyze the obtained data, verify it with one or more methods, and determine its accuracy. In this study, in vitro, in vivo and in silico methods and protein-protein interaction databases used for determination of protein-protein interaction are examined. The pros and cons of detection methods were investigated and the advantages and disadvantages of the methods were shared. The information contained in the databases was compared, investigated the similarity rates and reasons.

Keywords

PPI databases, PPI detection methods, Protein-protein interaction, Protein

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