Curated compendium of human transcriptional biomarker data.

Title

Curated compendium of human transcriptional biomarker data.

Creator

Golightly Nathan P; Bell Avery; Bischoff Anna I; Hollingsworth Parker D; Piccolo Stephen R

Publisher

Scientific data

Date

2018
2018-04

Description

One important use of genome-wide transcriptional profiles is to identify relationships between transcription levels and patient outcomes. These translational insights can guide the development of biomarkers for clinical application. Data from thousands of translational-biomarker studies have been deposited in public repositories, enabling reuse. However, data-reuse efforts require considerable time and expertise because transcriptional data are generated using heterogeneous profiling technologies, preprocessed using diverse normalization procedures, and annotated in non-standard ways. To address this problem, we curated 45 publicly available, translational-biomarker datasets from a variety of human diseases. To increase the data's utility, we reprocessed the raw expression data using a uniform computational pipeline, addressed quality-control problems, mapped the clinical annotations to a controlled vocabulary, and prepared consistently structured, analysis-ready data files. These data, along with scripts we used to prepare the data, are available in a public repository. We believe these data will be particularly useful to researchers seeking to perform benchmarking studies-for example, to compare and optimize machine-learning algorithms' ability to predict biomedical outcomes.

Subject

*Biomarkers; *Transcription; Databases; Disease/genetics; Gene Expression Profiling; Genetic; Humans

Rights

Article information provided for research and reference use only. All rights are retained by the journal listed under publisher and/or the creator(s).

Pages

180066–180066

Volume

5

Citation

Golightly Nathan P; Bell Avery; Bischoff Anna I; Hollingsworth Parker D; Piccolo Stephen R, “Curated compendium of human transcriptional biomarker data.,” NEOMED Bibliography Database, accessed July 1, 2022, https://neomed.omeka.net/items/show/4001.

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