Sains Malaysiana 47(12)(2018): 2933–2940

http://dx.doi.org/10.17576/jsm-2018-4712-01

 

Construction and Analysis of Protein-Protein Interaction Network to Identify the Molecular Mechanism in Laryngeal Cancer

(Pembinaan dan Analisis Jaringan Interaksi Protein-Protein untuk Mengenal Pasti Mekanisme Molekul Kanser Larinks)

 

SARAHANI HARUN¹ & NURULISA ZULKIFLE²*

 

¹Centre for Bioinformatics Research, Institute of Systems Biology (INBIOSIS), Universiti Kebangsaan Malaysia, 43600 UKM Bangi, Selangor Darul Ehsan, Malaysia

 

²Cluster for Oncological & Radiological Sciences, Advanced Medical & Dental Institute, Universiti Sains Malaysia, 13200 Bertam, Penang, Malaysia

 

Received: 30 May 2018/Accepted: 13 September 2018

 

ABSTRACT

Laryngeal cancer is the most common head and neck cancer in the world and its incidence is on the rise. However, the molecular mechanism underlying laryngeal cancer pathogenesis is poorly understood. The goal of this study was to develop a protein-protein interaction (PPI) network for laryngeal cancer to predict the biological pathways that underlie the molecular complexes in the network. Genes involved in laryngeal cancer were extracted from the OMIM database and their interaction partners were identified via text and data mining using Agilent Literature Search, STRING and GeneMANIA. PPI network was then integrated and visualised using Cytoscape ver3.6.0. Molecular complexes in the network were predicted by MCODE plugin and functional enrichment analyses of the molecular complexes were performed using BiNGO. 28 laryngeal cancer-related genes were present in the OMIM database. The PPI network associated with laryngeal cancer contained 161 nodes, 661 edges and five molecular complexes. Some of the complexes were related to the biological behaviour of cancer, providing the foundation for further understanding of the mechanism of laryngeal cancer development and progression.

 

Keywords: Functional enrichment analysis; laryngeal cancer; protein-protein interaction network; text mining

 

ABSTRAK

Kanser larinks adalah kanser kepala dan leher yang paling biasa di dunia dan kejadiannya semakin meningkat. Walau bagaimanapun, mekanisme molekul yang terlibat dalam patogenesis kanser larinks masih kurang difahami. Tujuan kajian ini dijalankan adalah untuk membangunkan jaringan interaksi protein-protein (IPP) bagi kanser larinks untuk meramal tapak jalan biologi menerusi analisis kompleks molekul daripada dalam jaringan IPP yang dibina. Gen yang terlibat dalam kanser larinks telah diekstrak daripada pangkalan data OMIM dan pasangan interaksinya telah dikenal pasti melalui pencarian teks dan data menggunakan Agilent Literature Search, STRING dan GeneMANIA. Jaringan IPP kemudiannya digabung dan divisualisasikan menggunakan Cytoscape ver3.6.0. Kompleks molekul dalam jaringan diramalkan oleh plugin MCODE dan analisis pengkayaan berfungsi kompleks molekul dilakukan menggunakan BiNGO. 28 gen berkaitan dengan kanser larinks ditemui dalam pangkalan data OMIM. Jaringan IPP yang dikaitkan dengan kanser larinks mengandungi 161 nodus, 661 interaksi dan lima kompleks molekul. Beberapa kompleks didapati berkaitan dengan tingkah laku biologi kanser dan ini telah menyediakan asas untuk memahami lebih lanjut mekanisme dalam pembangunan dan perkembangan kanser larinks.

 

Kata kunci: Analisis pengayaan berfungsi; jaringan interaksi protein-protein; kanser larinks; pencarian teks

 

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*Corresponding author; email: nurulisa@usm.my