A substrate-based ontology for human solute carriers.

Détails

ID Serval
serval:BIB_A5649B056C99
Type
Article: article d'un périodique ou d'un magazine.
Collection
Publications
Titre
A substrate-based ontology for human solute carriers.
Périodique
Molecular systems biology
Auteur(s)
Meixner E., Goldmann U., Sedlyarov V., Scorzoni S., Rebsamen M., Girardi E., Superti-Furga G.
ISSN
1744-4292 (Electronic)
ISSN-L
1744-4292
Statut éditorial
Publié
Date de publication
07/2020
Peer-reviewed
Oui
Volume
16
Numéro
7
Pages
e9652
Langue
anglais
Notes
Publication types: Journal Article
Publication Status: ppublish
Résumé
Solute carriers (SLCs) are the largest family of transmembrane transporters in the human genome with more than 400 members. Despite the fact that SLCs mediate critical biological functions and several are important pharmacological targets, a large proportion of them is poorly characterized and present no assigned substrate. A major limitation to systems-level de-orphanization campaigns is the absence of a structured, language-controlled chemical annotation. Here we describe a thorough manual annotation of SLCs based on literature. The annotation of substrates, transport mechanism, coupled ions, and subcellular localization for 446 human SLCs confirmed that ~30% of these were still functionally orphan and lacked known substrates. Application of a substrate-based ontology to transcriptomic datasets identified SLC-specific responses to external perturbations, while a machine-learning approach based on the annotation allowed us to identify potential substrates for several orphan SLCs. The annotation is available at https://opendata.cemm.at/gsflab/slcontology/. Given the increasing availability of large biological datasets and the growing interest in transporters, we expect that the effort presented here will be critical to provide novel insights into the functions of SLCs.
Mots-clé
SLCs, annotation, de-orphanization, ontology, solute carriers
Pubmed
Open Access
Oui
Création de la notice
11/08/2020 17:06
Dernière modification de la notice
13/08/2020 6:26
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