ArticleNucleic acids research2023
GPSAdb: a comprehensive web resource for interactive exploration of genetic perturbation RNA-seq datasets.
Article in Nucleic acids research, 2023. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 32 papers.
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Who cites it
32 citing papers in PubMed.
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- The dysregulation score method identifies epigenetic regulator genes that predict cancer prognosis and efficiency of cancer immunotherapy.Molecular therapy. Nucleic acids · 2025Article
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- LncRNA MEG3/CTCF-CXCR4 axis functions in the regulation of breast cancer cell migration.Non-coding RNA research · 2025Article
- NRF2-mediated persistent adaptation of oesophageal adenocarcinoma cells to HER2 inhibition.Oncogene · 2025Article
- A novel, synthesized, amphiphilic ethylene glycol squalene derivative suppresses BBN-induced bladder carcinogenesis.Scientific reports · 2025Article
- Machine learning-based in-silico analysis identifies signatures of lysyl oxidases for prognostic and therapeutic response prediction in cancer.Cell communication and signaling : CCS · 2025Article
- Molecular subtyping of renal clear cell carcinoma based on prognostic RASSF family genes and validation of C1QL1 as a key prognostic marker.Scientific reports · 2025Article
- Cell-free epigenomes enhanced fragmentomics-based model for early detection of lung cancer.Clinical and translational medicine · 2025Article
- Ionizing radiation-induced disruption of Rela-Bclaf1-spliceosome regulatory axis in primary spermatocytes causing spermatogenesis dysfunction.Cell communication and signaling : CCS · 2025Article
- Baicalein Inhibits Proliferation, Migration, and Invasion of Mesothelioma Cells Through the p53-FOXM1 Signaling Axis.Cancer management and research · 2025Article
- Chaperonins in Hepatocellular Carcinoma: Unveiling Their Role in Tumor Proliferation and Immune Modulation Through Multiomics Analysis.International journal of genomics · 2025Article
- Uridine-cytidine kinase 2 is correlated with immune, DNA damage repair and promotion of cancer stemness in pan-cancer.Frontiers in oncology · 2025Article
- Cooperative targeting of NF-κB enhances ferroptosis-driven HCC therapy with Alisertib and Donafenib.Frontiers in cell and developmental biology · 2025Article
- Immune alterations and overexpression of CTCF in endometrial carcinoma: insights from molecular subtyping.Cancer cell international · 2024Article
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Authors and funding
10 authors.
Funding
Abstract
Gene knock-out/down methods are commonly used to explore the functions of genes of interest, but a database that systematically collects perturbed data is not available currently. Manual curation of all the available human cell line perturbed RNA-seq datasets enabled us to develop a comprehensive human perturbation database (GPSAdb, https://www.gpsadb.com/). The current version of GPSAdb collected 3048 RNA-seq datasets associated with 1458 genes, which were knocked out/down by siRNA, shRNA, CRISPR/Cas9, or CRISPRi. The database provides full exploration of these datasets and generated 6096 new perturbed gene sets (up and down separately). GPSAdb integrated the gene sets and developed an online tool, genetic perturbation similarity analysis (GPSA), to identify candidate causal perturbations from differential gene expression data. In summary, GPSAdb is a powerful platform that aims to assist life science researchers to easily access and analyze public perturbed data and explore differential gene expression data in depth.
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Registered trials
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