PINA 3.0: mining cancer interactome
Open accessAbstract
Protein–protein interactions (PPIs) are crucial to mediate biological functions, and understanding PPIs in cancer type-specific context could help decipher the underlying molecular mechanisms of tumorigenesis and identify potential therapeutic options. Therefore, we update the Protein Interaction Network Analysis (PINA) platform to version 3.0, to integrate the unified human interactome with RNA-seq transcriptomes and mass spectrometry-based proteomes across tens of cancer types. A number of new analytical utilities were developed to help characterize the cancer context for a PPI network, which includes inferring proteins with expression specificity and identifying candidate prognosis biomarkers, putative cancer drivers, and therapeutic targets for a specific cancer type; as well as identifying pairs of co-expressing interacting proteins across cancer types. Furthermore, a brand-new web interface has been designed to integrate these new utilities within an interactive network visualization environment, which allows users to quickly and comprehensively investigate the roles of human interacting proteins in a cancer type-specific context. PINA is freely available at https://omics.bjcancer.org/pina/.
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- Authors
- Du, Y., Cai, M., Xing, X., Ji, J., Yang, E., & Wu, J.
- Affiliations
- Peking University Cancer Hospital (CN)
- Peking University (CN)
- Corresponding author
- Yang, Ence
- Wu, Jianmin
- Venue
- Nucleic Acids Research
- Publisher
- Oxford University Press (OUP)
- Published
- 2020-11-24
- Volume
- 49
- Issue
- D1
- Pages
- D1351-D1357
- ISSN
- 0305-1048 (ISSN-L)
- 1362-4962
- PMC
- PMC7779002
- OpenAlex
- W3108941912
- Cited by
- 60
- References
- 34
- Citations by year
- 2026: 6 · 2025: 19 · 2024: 8 · 2023: 9 · 2022: 13 · 2021: 5
- FWCI
- 2.19
- Type
- journal article
- Language
- en
- Open access
- gold
- doi.org
- Licence
- Locations
- Nucleic Acids Research (publishedVersion, cc-by)
- PubMed Central (publishedVersion, cc-by)
- PubMed (publishedVersion)
- Funders
- PKU-Baidu Fund (2019BD012)
- Beijing Municipal Science and Technology Commission (Z201100008320006)
- Beijing Municipal Bureau of Health (2019-1)
- Topics
- Life Sciences › Biochemistry, Genetics and Molecular Biology › Molecular Biology › Bioinformatics and Genomic Networks
- Life Sciences › Biochemistry, Genetics and Molecular Biology › Cell Biology › Biotin and Related Studies
- Life Sciences › Biochemistry, Genetics and Molecular Biology › Cancer Research › Cancer-related molecular mechanisms research
- Keywords
- protein-protein interaction, human interactome, prognostic factors, cancer drivers, therapeutic target, network visualization
- MeSH terms
- Algorithms, Humans, Mutation, Neoplasm Proteins, Neoplasms, Software, Gene Expression Regulation, Neoplastic, Survival Analysis, Internet, Protein Interaction Mapping, Databases, Protein, Metabolic Networks and Pathways, Data Mining, Molecular Sequence Annotation, Transcriptome, Exome, Protein Interaction Maps, Carcinogenesis
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