ReviewBriefings in bioinformatics2016
Public data and open source tools for multi-assay genomic investigation of disease.
Review in Briefings in bioinformatics, 2016. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 28 papers, 1 of them a synthesis that pooled it.
What it found
Each row is one number read from the abstract, on the scale the paper reported it, with its interval. Left of the dashed line favours the treatment, right favours the comparator. Under each row is the sentence it came from. New to these charts? A ten-minute tutorial.
The abstract states no effect estimate the extractor could read, or names no intervention and outcome on the map, so this paper lights no cell and moves no belief. It is still indexed, cited and linked below.
The trial behind it
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.
Neither the registry nor the abstract names a trial number. If this is a trial report, that itself is worth knowing.
Who cites it
28 citing papers in PubMed, 1 synthesis or guideline pooled it.
- Computational resources associating diseases with genotypes, phenotypes and exposures.Briefings in bioinformatics · 2019Pooled it
- Multimodal analysis methods in predictive biomedicine.Computational and structural biotechnology journal · 2023Review
- Large-Scale Databases and Portals on Cancer Genome to Analyze Chaperone Genes Correlated to Patient Prognosis.Methods in molecular biology (Clifton, N.J.) · 2023Article
- STATegra: Multi-Omics Data Integration - A Conceptual Scheme With a Bioinformatics Pipeline.Frontiers in genetics · 2021Article
- Omics Integration Analysis Unravel the Landscape of Driving Mechanisms of Colorectal Cancer.Asian Pacific journal of cancer prevention : APJCP · 2020Article
- Multiomic Integration of Public Oncology Databases in Bioconductor.JCO clinical cancer informatics · 2020Article
- Vertical and horizontal integration of multi-omics data with miodin.BMC bioinformatics · 2019Article
- Bringing radiomics into a multi-omics framework for a comprehensive genotype-phenotype characterization of oncological diseases.Journal of translational medicine · 2019Review
- The metaRbolomics Toolbox in Bioconductor and beyond.Metabolites · 2019Review
- Bioinformatics-based discovery of PYGM and TNNC2 as potential biomarkers of head and neck squamous cell carcinoma.Bioscience reports · 2019Article
- MetaGxData: Clinically Annotated Breast, Ovarian and Pancreatic Cancer Datasets and their Use in Generating a Multi-Cancer Gene Signature.Scientific reports · 2019Article
- Metabolic gene NR4A1 as a potential therapeutic target for non-smoking female non-small cell lung cancer patients.Thoracic cancer · 2019Article
- Low expression of KCNN3 may affect drug resistance in ovarian cancer.Molecular medicine reports · 2018Article
- A review of connectivity map and computational approaches in pharmacogenomics.Briefings in bioinformatics · 2018Review
- Training replicable predictors in multiple studies.Proceedings of the National Academy of Sciences of the United States of America · 2018Article
- Genome, transcriptome and proteome: the rise of omics data and their integration in biomedical sciences.Briefings in bioinformatics · 2018Review
- Systems Medicine Disease: Disease Classification and Scalability Beyond Networks and Boundary Conditions.Frontiers in bioengineering and biotechnology · 2018Article
- Epigenetic regulation of gene expression in cancer: techniques, resources and analysis.Briefings in functional genomics · 2018Article
- Review of Statistical Learning Methods in Integrated Omics Studies (An Integrated Information Science).Bioinformatics and biology insights · 2018Review
- Large-scale analysis reveals a novel risk score to predict overall survival in hepatocellular carcinoma.Cancer management and research · 2018Article
Corrections and comments
PubMed lists nothing against this paper. Absence here is not a guarantee, only a check that was made.
Authors and funding
15 authors.
Funding
Abstract
Molecular interrogation of a biological sample through DNA sequencing, RNA and microRNA profiling, proteomics and other assays, has the potential to provide a systems level approach to predicting treatment response and disease progression, and to developing precision therapies. Large publicly funded projects have generated extensive and freely available multi-assay data resources; however, bioinformatic and statistical methods for the analysis of such experiments are still nascent. We review multi-assay genomic data resources in the areas of clinical oncology, pharmacogenomics and other perturbation experiments, population genomics and regulatory genomics and other areas, and tools for data acquisition. Finally, we review bioinformatic tools that are explicitly geared toward integrative genomic data visualization and analysis. This review provides starting points for accessing publicly available data and tools to support development of needed integrative methods.
Indexed as
Identifiers
What OpenQuestion holds
Registered trials
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.