A substrate-based ontology for human solute carriers.

Details

Serval ID
serval:BIB_A5649B056C99
Type
Article: article from journal or magazin.
Collection
Publications
Title
A substrate-based ontology for human solute carriers.
Journal
Molecular systems biology
Author(s)
Meixner E., Goldmann U., Sedlyarov V., Scorzoni S., Rebsamen M., Girardi E., Superti-Furga G.
ISSN
1744-4292 (Electronic)
ISSN-L
1744-4292
Publication state
Published
Issued date
07/2020
Peer-reviewed
Oui
Volume
16
Number
7
Pages
e9652
Language
english
Notes
Publication types: Journal Article
Publication Status: ppublish
Abstract
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.
Keywords
SLCs, annotation, de-orphanization, ontology, solute carriers
Pubmed
Open Access
Yes
Create date
11/08/2020 16:06
Last modification date
13/08/2020 5:26
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