ArticleBioinformatics (Oxford, England)2020
SurfaceGenie: a web-based application for prioritizing cell-type-specific marker candidates.
Article in Bioinformatics (Oxford, England), 2020. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 39 papers.
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Trials whose registry record cites this paper, or whose number appears in the abstract. A trial that started after this paper was published is citing it as background, not reporting it.
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Who cites it
39 citing papers in PubMed.
- Enrichment and Proteomic Profiling of Stromal-Associated Extracellular Vesicle Subpopulations From Arthritic Synovial Fluid by Size-Exclusion Chromatography Coupled to CD90-Directed Immunocapture.Journal of extracellular vesicles · 2026Article
- Protocol for N-glycoproteomic enrichment of cancer cell-surface proteins in patient-derived xenografts.STAR protocols · 2026Article
- Surface Proteomics of Cancer-Derived Extracellular Vesicles Reveals Universal Heat Shock Proteins and Cancer Signatures.Molecular & cellular proteomics : MCP · 2026Article
- GPNMB-directed CAR T cell therapy against MiT/TFE-family fusion-driven solid tumors.Nature cancer · 2026Article
- Pan-cancer N-glycoproteomic atlas of patient-derived xenografts uncovers FAT2 as an actionable surface target.Cell reports. Medicine · 2026Article
- CellMiner cross-database (CellMinerCDB) version 2.2 for explorations of patient-derived cancer cell line pharmacogenomics.Nucleic acids research · 2026Article
- A molecular map of the human spinal dorsal and ventral horn defines arrangement of neuronal types and glial sex differences.bioRxiv : the preprint server for biology · 2025Article
- SurfR: Riding the wave of RNA-seq data with a comprehensive bioconductor package to identify surface protein-coding genes.Bioinformatics advances · 2025Article
- Immune System-Related Plasma Pathogenic Extracellular Vesicle Subpopulations Predict Osteoarthritis Progression.International journal of molecular sciences · 2024Article
- A proteogenomic surfaceome study identifies DLK1 as an immunotherapeutic target in neuroblastoma.Cancer cell · 2024Article
- Unveiling Tumorigenesis Mechanisms and Drug Therapy in Neuroblastoma by Mass Spectrometry Based Proteomics.Children (Basel, Switzerland) · 2024Review
- Cancer pharmacoinformatics: Databases and analytical tools.Functional & integrative genomics · 2024Review
- Single-cell RNA sequencing of pediatric Hodgkin lymphoma to study the inhibition of T cell subtypes.HemaSphere · 2024Article
- Veneer Is a Webtool for Rapid, Standardized, and Transparent Interpretation, Annotation, and Reporting of Mammalian Cell SurfaceJournal of proteome research · 2024Article
- Prostate cancer reshapes the secreted and extracellular vesicle urinary proteomes.Nature communications · 2024Article
- Zinc-chelating BET bromodomain inhibitors equally target islet endocrine cell types.American journal of physiology. Regulatory, integrative and comparative physiology · 2024Article
- The landscape of immune dysregulation in pediatric sepsis at a single-cell resolution.Clinical immunology (Orlando, Fla.) · 2024Article
- Droplet-based proteomics reveals CD36 as a marker for progenitors in mammary basal epithelium.Cell reports methods · 2024Article
- Organelle resolved proteomics uncovers PLA2R1 as a novel cell surface marker required for chordoma growth.Acta neuropathologica communications · 2024Article
- Surface and Global Proteome Analyses Identify ENPP1 and Other Surface Proteins as Actionable Immunotherapeutic Targets in Ewing Sarcoma.Clinical cancer research : an official journal of the American Association for Cancer Research · 2024Article
Corrections and comments
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Authors and funding
7 authors.
Funding
Abstract
motivationCell-type-specific surface proteins can be exploited as valuable markers for a range of applications including immunophenotyping live cells, targeted drug delivery and in vivo imaging. Despite their utility and relevance, the unique combination of molecules present at the cell surface are not yet described for most cell types. A significant challenge in analyzing 'omic' discovery datasets is the selection of candidate markers that are most applicable for downstream applications.
resultsHere, we developed GenieScore, a prioritization metric that integrates a consensus-based prediction of cell surface localization with user-input data to rank-order candidate cell-type-specific surface markers. In this report, we demonstrate the utility of GenieScore for analyzing human and rodent data from proteomic and transcriptomic experiments in the areas of cancer, stem cell and islet biology. We also demonstrate that permutations of GenieScore, termed IsoGenieScore and OmniGenieScore, can efficiently prioritize co-expressed and intracellular cell-type-specific markers, respectively. AVAILABILITY AND IMPLEMENTATION: Calculation of GenieScores and lookup of SPC scores is made freely accessible via the SurfaceGenie web application: www.cellsurfer.net/surfacegenie. CONTACT: Rebekah.gundry@unmc.edu. SUPPLEMENTARY INFORMATION: Supplementary data are available at Bioinformatics online.
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Read under generation 80e0d062 · epoch 390. Bibliography from PubMed, PubMed Central and OpenAlex; grants from NIH RePORTER; trial links from ClinicalTrials.gov; estimates, votes and beliefs from the OpenQuestion graph.