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- Title
TCGA-My: A Systematic Repository for Systems Biology of Malaysian Colorectal Cancer.
- Authors
Azuwar, Mohd Amin; Muhammad, Nor Azlan Nor; Afiqah-Aleng, Nor; Ab Mutalib, Nurul-Syakima; Md. Yusof, Najwa Farhah; Mohd Yunos, Ryia Illani; Ishak, Muhiddin; Saidin, Sazuita; Rose, Isa Mohamed; Sagap, Ismail; Mazlan, Luqman; Mohd Azman, Zairul Azwan; Mazlan, Musalmah; Ab Rahim, Sharaniza; Wan Ngah, Wan Zurinah; Nathan, Sheila; Hashim, Nurul Azmir Amir; Mohamed-Hussein, Zeti-Azura; Jamal, Rahman
- Abstract
Colorectal cancer (CRC) ranks second among the most commonly occurring cancers in Malaysia, and unfortunately, its pathobiology remains unknown. CRC pathobiology can be understood in detail with the implementation of omics technology that is able to generate vast amounts of molecular data. The generation of omics data has introduced a new challenge for data organization. Therefore, a knowledge-based repository, namely TCGA-My, was developed to systematically store and organize CRC omics data for Malaysian patients. TCGA-My stores the genome and metabolome of Malaysian CRC patients. The genome and metabolome datasets were organized using a Python module, pandas. The variants and metabolites were first annotated with their biological information using gene ontologies (GOs) vocabulary. The TCGA-My relational database was then built using HeidiSQL PorTable 9.4.0.512, and Laravel was used to design the web interface. Currently, TCGA-My stores 1,517,841 variants, 23,695 genes, and 167,451 metabolites from the samples of 50 CRC patients. Data entries can be accessed via search and browse menus. TCGA-My aims to offer effective and systematic omics data management, allowing it to become the main resource for Malaysian CRC research, particularly in the context of biomarker identification for precision medicine.
- Subjects
MALAYSIA; COLORECTAL cancer; MALAYSIANS; RELATIONAL databases; WEB design; INSTITUTIONAL repositories; SYSTEMS biology
- Publication
Life (2075-1729), 2022, Vol 12, Issue 6, p772
- ISSN
2075-1729
- Publication type
Article
- DOI
10.3390/life12060772