ArticleNucleic acids research2015
Integrated analysis of numerous heterogeneous gene expression profiles for detecting robust disease-specific biomarkers and proposing drug targets.
Article in Nucleic acids research, 2015. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 16 papers, 1 of them a synthesis that pooled it.
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Who cites it
16 citing papers in PubMed, 1 synthesis or guideline pooled it.
- The landscape of the methodology in drug repurposing using human genomic data: a systematic review.Briefings in bioinformatics · 2024Pooled it
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- Quencher-free CRISPR-based molecular detection using an amphiphilic DNA fluorescence probe.Biosensors & bioelectronics · 2025Article
- Protein-protein interaction prediction using bidirectional GRUs with explicit ensemble.PloS one · 2025Article
- Characterizing the Expression Patterns of Parkinson's Disease Associated Genes.Frontiers in neuroscience · 2021Article
- Familial/inherited cancer syndrome: a focus on the highly consanguineous Arab population.NPJ genomic medicine · 2020Review
- Prioritizing Gene Cascading Paths to Model Colorectal Cancer Through Engineered Organoids.Frontiers in bioengineering and biotechnology · 2020Article
- A Computational Framework for Genome-wide Characterization of the Human Disease Landscape.Cell systems · 2019Article
- Evaluation of Pathway Activation for a Single Sample Toward Inflammatory Bowel Disease Classification.Frontiers in genetics · 2019Article
- Association between expression of random gene sets and survival is evident in multiple cancer types and may be explained by sub-classification.PLoS computational biology · 2018Article
- Immunogenetics of glioblastoma: the future of personalized patient management.NPJ precision oncology · 2018Review
- Precision annotation of digital samples in NCBI's gene expression omnibus.Scientific data · 2017Article
- Extracting replicable associations across multiple studies: Empirical Bayes algorithms for controlling the false discovery rate.PLoS computational biology · 2017Article
- Utilizing somatic mutation data from numerous studies for cancer research: proof of concept and applications.Oncogene · 2017Article
- Article
- ONE-CLASS DETECTION OF CELL STATES IN TUMOR SUBTYPES.Pacific Symposium on Biocomputing. Pacific Symposium on Biocomputing · 2016Article
Corrections and comments
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4 authors.
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No grant is acknowledged in the PubMed record.
Abstract
Genome-wide expression profiling has revolutionized biomedical research; vast amounts of expression data from numerous studies of many diseases are now available. Making the best use of this resource in order to better understand disease processes and treatment remains an open challenge. In particular, disease biomarkers detected in case-control studies suffer from low reliability and are only weakly reproducible. Here, we present a systematic integrative analysis methodology to overcome these shortcomings. We assembled and manually curated more than 14,000 expression profiles spanning 48 diseases and 18 expression platforms. We show that when studying a particular disease, judicious utilization of profiles from other diseases and information on disease hierarchy improves classification quality, avoids overoptimistic evaluation of that quality, and enhances disease-specific biomarker discovery. This approach yielded specific biomarkers for 24 of the analyzed diseases. We demonstrate how to combine these biomarkers with large-scale interaction, mutation and drug target data, forming a highly valuable disease summary that suggests novel directions in disease understanding and drug repurposing. Our analysis also estimates the number of samples required to reach a desired level of biomarker stability. This methodology can greatly improve the exploitation of the mountain of expression profiles for better disease analysis.
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