Evaluation of Sub-Network search programs in epilepsy-related GWAS dataset

Beyhan ADANUR DEDETURK, (Bilgisayar Mühendisliği, Mühendislik Fakültesi, Abdullah Gül Üniversitesi, Kayseri, Türkiye.)
Burcu BAKİR GUNGOR (Bilgisayar Mühendisliği, Mühendislik Fakültesi, Abdullah Gül Üniversitesi, Kayseri, Türkiye.)
Pamukkale Üniversitesi Mühendislik Bilimleri Dergisi
17 3
Yıl: 2022 Cilt: 28 Sayı: 2 Sayfa Aralığı: 292 - 298 Metin Dili: İngilizce DOI: 10.5505/pajes.2021.56424 İndeks Tarihi: 25-06-2022

Evaluation of Sub-Network search programs in epilepsy-related GWAS dataset

Öz:
The active sub-network detection aims to find a group of interconnected genes of disease-related genes in a protein-protein interaction network. In recent years, several algorithms have been developed for this problem. In this study, the analysis of disease-specific sub-network identification programs is evaluated using epilepsy data set. Under the same conditions and with the same data set, 9 different programs are run and results of their Greedy algorithm, Genetic algorithm, Simulated Annealing Algorithm, MCC (Maximal Clique Centrality) algorithm, MCODE (Molecular Complex Detection) algorithm, and PEWCC (Protein Complex Detection using Weighted Clustering Coefficient) algorithm are shown. The top-scoring 5 modules of each program, are compared using fold enrichment analysis and normalized mutual information. Also, the identified subnetworks are functionally enriched using a hypergeometric test, and hence, disease-associated biological pathways are identified. In addition, running times and features of the programs are comparatively evaluated
Anahtar Kelime:

Epilepsi ile ilgili GWAS veri kümesinde alt ağ arama programlarının değerlendirmesi

Öz:
Aktif alt ağ tespiti, bir protein-protein etkileşim ağında hastalıkla ilgili genlerin birbirine bağlı bir grup genini bulmayı amaçlamaktadır. Son yıllarda bu problem için çeşitli algoritmalar geliştirilmiştir. Bu çalışmada, hastalığa özgü alt ağ tanımlama programlarının analizleri epilepsi veri seti kullanılarak değerlendirilmiştir. Aynı koşullar altında ve aynı veri seti ile 9 farklı program çalıştırılmış ve bu programların Greedy algoritması, Genetik algoritma, Simüle Tavlama Algoritması, MCC (Maximal Clique Centrality) algoritması, MCODE (Molecular Complex Detection) algoritması ve PEWCC (Protein Complex) Ağırlıklı Kümeleme Katsayısı) algoritması sonuçları gösterilmiştir. Her programın en yüksek puan alan 5 modülü, kat zenginleştirme analizi ve normalleştirilmiş karşılıklı bilgi kullanılarak karşılaştırılmıştır. Aynı zamanda tanımlanan alt ağlar, hipergeometrik test kullanılarak fonksiyonel olarak zenginleştirilmiş ve hastalıkla ilişkili biyolojik yollar belirlenmeye çalışılmıştır. Ayrıca programların çalışma süreleri ve özellikleri karşılaştırmalı olarak değerlendirilmiştir.
Anahtar Kelime:

Belge Türü: Makale Makale Türü: Düzeltme Erişim Türü: Erişime Açık
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APA DEDETURK B, GUNGOR B (2022). Evaluation of Sub-Network search programs in epilepsy-related GWAS dataset. , 292 - 298. 10.5505/pajes.2021.56424
Chicago DEDETURK Beyhan ADANUR,GUNGOR Burcu BAKİR Evaluation of Sub-Network search programs in epilepsy-related GWAS dataset. (2022): 292 - 298. 10.5505/pajes.2021.56424
MLA DEDETURK Beyhan ADANUR,GUNGOR Burcu BAKİR Evaluation of Sub-Network search programs in epilepsy-related GWAS dataset. , 2022, ss.292 - 298. 10.5505/pajes.2021.56424
AMA DEDETURK B,GUNGOR B Evaluation of Sub-Network search programs in epilepsy-related GWAS dataset. . 2022; 292 - 298. 10.5505/pajes.2021.56424
Vancouver DEDETURK B,GUNGOR B Evaluation of Sub-Network search programs in epilepsy-related GWAS dataset. . 2022; 292 - 298. 10.5505/pajes.2021.56424
IEEE DEDETURK B,GUNGOR B "Evaluation of Sub-Network search programs in epilepsy-related GWAS dataset." , ss.292 - 298, 2022. 10.5505/pajes.2021.56424
ISNAD DEDETURK, Beyhan ADANUR - GUNGOR, Burcu BAKİR. "Evaluation of Sub-Network search programs in epilepsy-related GWAS dataset". (2022), 292-298. https://doi.org/10.5505/pajes.2021.56424
APA DEDETURK B, GUNGOR B (2022). Evaluation of Sub-Network search programs in epilepsy-related GWAS dataset. Pamukkale Üniversitesi Mühendislik Bilimleri Dergisi, 28(2), 292 - 298. 10.5505/pajes.2021.56424
Chicago DEDETURK Beyhan ADANUR,GUNGOR Burcu BAKİR Evaluation of Sub-Network search programs in epilepsy-related GWAS dataset. Pamukkale Üniversitesi Mühendislik Bilimleri Dergisi 28, no.2 (2022): 292 - 298. 10.5505/pajes.2021.56424
MLA DEDETURK Beyhan ADANUR,GUNGOR Burcu BAKİR Evaluation of Sub-Network search programs in epilepsy-related GWAS dataset. Pamukkale Üniversitesi Mühendislik Bilimleri Dergisi, vol.28, no.2, 2022, ss.292 - 298. 10.5505/pajes.2021.56424
AMA DEDETURK B,GUNGOR B Evaluation of Sub-Network search programs in epilepsy-related GWAS dataset. Pamukkale Üniversitesi Mühendislik Bilimleri Dergisi. 2022; 28(2): 292 - 298. 10.5505/pajes.2021.56424
Vancouver DEDETURK B,GUNGOR B Evaluation of Sub-Network search programs in epilepsy-related GWAS dataset. Pamukkale Üniversitesi Mühendislik Bilimleri Dergisi. 2022; 28(2): 292 - 298. 10.5505/pajes.2021.56424
IEEE DEDETURK B,GUNGOR B "Evaluation of Sub-Network search programs in epilepsy-related GWAS dataset." Pamukkale Üniversitesi Mühendislik Bilimleri Dergisi, 28, ss.292 - 298, 2022. 10.5505/pajes.2021.56424
ISNAD DEDETURK, Beyhan ADANUR - GUNGOR, Burcu BAKİR. "Evaluation of Sub-Network search programs in epilepsy-related GWAS dataset". Pamukkale Üniversitesi Mühendislik Bilimleri Dergisi 28/2 (2022), 292-298. https://doi.org/10.5505/pajes.2021.56424
Sayfa Oluşturulma Tarihi
23-04-2024 23:33

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