ArticleIET systems biology2018
SMILE: a novel procedure for subcellular module identification with localisation expansion.
Article in IET systems biology, 2018. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 14 papers.
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Who cites it
14 citing papers in PubMed.
- Large-scale transcriptome analysis reveals KIF20A as a novel indicator of cisplatin resistance in high-grade serous ovarian cancer.Journal of ovarian research · 2026Article
- Deep learning model to discriminate diverse infection types based on pairwise analysis of host gene expression.iScience · 2024Article
- Co-expression module analysis reveals high expression homogeneity for both coding and non-coding genes in sepsis.BMC genomics · 2023Article
- Deciphering associations between gut microbiota and clinical factors using microbial modules.Bioinformatics (Oxford, England) · 2023Article
- bvnGPS: a generalizable diagnostic model for acute bacterial and viral infection using integrative host transcriptomics and pretrained neural networks.Bioinformatics (Oxford, England) · 2023Article
- Long non-coding RNA pairs to assist in diagnosing sepsis.BMC genomics · 2021Article
- Blood Circulating miRNA Pairs as a Robust Signature for Early Detection of Esophageal Cancer.Frontiers in oncology · 2021Article
- Article
- Whole blood transcriptomic investigation identifies long non-coding RNAs as regulators in sepsis.Journal of translational medicine · 2020Article
- Knockdown of lncRNA MALAT1 Alleviates LPS-Induced Acute Lung Injury via Inhibiting Apoptosis Through the miR-194-5p/FOXP2 Axis.Frontiers in cell and developmental biology · 2020Article
- Exploiting locational and topological overlap model to identify modules in protein interaction networks.BMC bioinformatics · 2019Article
- Normalization Methods for the Analysis of Unbalanced Transcriptome Data: A Review.Frontiers in bioengineering and biotechnology · 2019Review
- Selected research articles from the 2017 International Workshop on Computational Network Biology: Modeling, Analysis, and Control (CNB-MAC).BMC bioinformatics · 2018Article
- Biochemical pathway analysis of gastric atrophy.Gastroenterology and hepatology from bed to bench · 2018Article
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Authors and funding
3 authors.
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Abstract
Computational clustering methods help identify functional modules in protein-protein interaction (PPI) network, in which proteins participate in the same biological pathways or specific functions. Subcellular localisation is crucial for proteins to implement biological functions and each compartment accommodates specific portions of the protein interaction structure. However, the importance of protein subcellular localisation is often neglected in the studies of module identification. In this study, the authors propose a novel procedure, subcellular module identification with localisation expansion (SMILE), to identify super modules that consist of several subcellular modules performing specific biological functions among cell compartments. These super modules identified by SMILE are more functionally diverse and have been verified to be more associated with known protein complexes and biological pathways compared with the modules identified from the global PPI networks in both the compartmentalised PPI and InWeb_InBioMap datasets. The authors' results reveal that subcellular localisation is a principal feature of functional modules and offers important guidance in detecting biologically meaningful results.
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