PUBLICATION
Enhanced Over-Representation Analysis for the Differential Regulation of Birc5a and HIF2α-Knockdown Approaches
- Authors
- Liu, C.C., Shih, T.C., Pai, T.W., Hu, C.H., Tzou, W.S.
- ID
- ZDB-PUB-210130-7
- Date
- 2021
- Source
- Journal of computational biology : a journal of computational molecular cell biology 28(7): 674-686 (Journal)
- Registered Authors
- Keywords
- RNA-seq, differential expression, hypoxia-inducible factors, long non-coding RNA, surviving
- MeSH Terms
-
- Algorithms
- Animals
- Basic Helix-Loop-Helix Transcription Factors/genetics*
- Gene Expression Profiling/methods*
- Gene Expression Regulation, Developmental
- Gene Knockdown Techniques
- Gene Regulatory Networks*
- High-Throughput Nucleotide Sequencing
- Sequence Analysis, RNA
- Survivin/genetics*
- Zebrafish/embryology*
- Zebrafish/genetics
- Zebrafish Proteins/genetics*
- PubMed
- 33512268 Full text @ J. Comput. Biol.
Citation
Liu, C.C., Shih, T.C., Pai, T.W., Hu, C.H., Tzou, W.S. (2021) Enhanced Over-Representation Analysis for the Differential Regulation of Birc5a and HIF2α-Knockdown Approaches. Journal of computational biology : a journal of computational molecular cell biology. 28(7):674-686.
Abstract
Hypoxia-inducible factors (HIFs) and survivin (Birc5) genes are often considered important cancer drug targets for molecularly targeted therapy, as both genes play important roles in the cellular differentiation and development of neuronal cells. Pathway enrichment analysis is predominantly applied when interpreting the correlated behaviors of activated gene clusters. Traditional enrichment analysis is evaluated via p-values only, regardless of gene expression fold-change levels, gene locations, and possible hidden interactions within a pathway. Here, we combined these factors to retrieve significant pathways, as compared with traditional approaches. We performed RNA-seq analyses on Birc5a and HIF2α knocked down in zebrafish during the embryogenesis stage. Regarding Birc5a, two additional biological pathways, sphingolipid metabolism and herpes simplex infection, were identified; whereas for HIF2α, four biological pathways were re-identified, including ribosome biogenesis in eukaryotes, proteasome, purine metabolism, and complement and coagulation cascades. Our proposed approaches identified additional significant pathways directly related to cell differentiation or cancer, also providing comprehensive mechanisms for designing further biological experiments.
Genes / Markers
Expression
Phenotype
Mutations / Transgenics
Human Disease / Model
Sequence Targeting Reagents
Fish
Orthology
Engineered Foreign Genes
Mapping