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Methods Mol Biol. 2019;1959:275-289. doi: 10.1007/978-1-4939-9164-8_18.

Designing an In Silico Strategy to Select Tissue-Leakage Biomarkers Using the Galaxy Framework.

Author information

1
Université Grenoble Alpes, CEA, Inserm, BGE U1038, Grenoble, France.
2
INRA, MAIAGE Unit, University Paris-Saclay, Jouy-en-Josas, France.
3
Université Grenoble Alpes, CEA, Inserm, BGE U1038, Grenoble, France. yves.vandenbrouck@cea.fr.

Abstract

Knowledge-based approaches using large-scale biological ("omics") data are a powerful way to identify mechanistic biomarkers, provided that scientists have access to computational solutions even when they have little programming experience or bioinformatics support. To achieve this goal, we designed a set of tools under the Galaxy framework to allow biologists to define their own strategy for reproducible biomarker selection. These tools rely on retrieving experimental data from public databases, and applying successive filters derived from information relating to disease pathophysiology. A step-by-step protocol linking these tools was implemented to select tissue-leakage biomarker candidates of myocardial infarction. A list of 24 candidates suitable for experimental assessment by MS-based proteomics is proposed. These tools have been made publicly available at http://www.proteore.org , allowing researchers to reuse them in their quest for biomarker discovery.

KEYWORDS:

Computer application; Galaxy; Human plasma; Proteomics; Tissue injury; Tissue-leakage biomarkers; Web server

PMID:
30852829
DOI:
10.1007/978-1-4939-9164-8_18
[Indexed for MEDLINE]

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