Open AccessBioinformatics Pathway Analysis Pipeline for NGS Transcriptome Profile Data on Nasopharyngeal Carcinoma
Author(s) -
Digdo Sudigyo,
Gisti Rahmawati,
Dicka Wahyu Setiasari,
Risky Hiskia Poluan,
Tjeng Wawan Cenggoro,
Arif Budiarto,
Alam Ahmad Hidayat,
Sri R. Indrasari,
FNU Afiahayati,
Sofia Mubarika Haryana,
Bens Pardamean
Publication year - 2021
Publication title -
iop conference series. earth and environmental science
Language(s) - English
Resource type - Journals
eISSN - 1755-1307
pISSN - 1755-1315
DOI - 10.1088/1755-1315/794/1/012115
Subject(s) - workflow , transcriptome , computer science , pipeline (software) , software , computational biology , raw data , bioinformatics , data mining , gene , biology , database , gene expression , genetics , operating system , programming language
Next-Generation Sequencing (NGS)-based genomics data have a huge potential to be used in transcriptomic profiling of Nasopharyngeal Carcinoma (NPC) to study the biosynthesis mechanism behind it. The high dimensionality of NGS data is the main challenge in performing the data analysis to extract useful information. In this workflow pipeline, memory-efficient Linux-based software such as HISAT2 and HTSeq are utilized to process the raw NGS data. Furthermore, Differential Expression Gene (DEG) list can be obtained by performing advanced analysis to the aligned Ribonucleic Acid (RNA) sequence using the edgeR protocol. This DEG list is one of the main inputs of biological pathway analysis that can be done in DAVID and PANTHER web-based software. Both tools generate a different pathway result related to inflammation.