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How to Cite Our Database

J. Y. Yin, Z. Chen, N. X. You, F. C. Li, H. Y. Zhang, J. Xue, H. Ma, Q. W. Zhao, L. S. Yu*, S. Zeng* & F. Zhu*. VARIDT 3.0: the phenotypic and regulatory variability of drug transporter. Nucleic Acids Research. 52(D1): D1490-D1502 (2024). PMID: 37819041

The Information Updated to the Latest VARIDT 4.0


425 transporters integrated in VARIDT4.0 were found to be closely related to the transportation of 889 approved, 221 clinical trial drugs and 689 endogenous metabolites, which involved widely in the treatment of 558 diseases.


VARIDT 4.0: A Three-Level Framework for Distribution Variability and a Comprehensive Data Update:

α. Tissue Distribution (TD) of DTs

 This module provides 25,797 tissue-level data points, detailing the expression of 404 transporters across 52 tissues. The data comprises 19,658 transcriptomic and 6,139 proteomic entries.

β. Cell Distribution (CD) of DTs

 This module contains 451,830 cell-level data points, providing the most granular view of transporter expression. The data is organized into three main types: Single-cell Transcriptomics: 51,644 entries for 401 transporters across 180 cell types; Cell Line Transcriptomics: 340,777 entries for 402 transporters across 1,201 cell lines; Cell Line Proteomics: 59,409 entries for 111 transporters across 949 cell lines.

γ. Organelle Distribution (OD) of DTs

 This module offers 1,034 subcellular localization entries for 422 transporters across 68 organelles. The dataset is composed of: Experimentally Validated: 593 records for 422 DTs; Computationally Predicted: 441 entries for 316 DTs.

δ. Update of Previous Versions

 In parallel with these new modules, all 197,592 entries from previous versions (v1.0-v3.0) have been systematically curated and re-mapped into the framework to ensure data continuity and integrity.

The Information Provided in the Previous Versions of VARIDT


Five Aspects of Phenotypic and Regulatory Variability are Provided for Each DT in VARIDT 3.0 (Graphic Illustration) :

α. Microbiota Influence (MBI) of DTs

2,072 MBI data of 145 DTs regulated by 124 microbe species, and the relative abundances of these microbe species across 76 diseases

β. Post-Translational Modification (PTM) of DTs

10,255 PTM data of 418 DTs that were related to 24 PTM types, and graphical illustrations on 9,717 experimentally-validated PTM sites

γ. Transcriptional Regulation (TSR) of DTs

10,610 TSR data of 381 DTs that were regulated by 357 TFs, and the differential expression profiles of these TFs across 59 organs and 106 diseases

δ. Epigenetic Regulation (EGR) of DTs

46,748 EGR data of 287 DTs related to 3 types of EGR

ε. Exogenous Modulation (EGM) of DTs

12,209 EGM data of 419 DTs modulated by 1,717 xenobiotics


Four Aspects of Structural Variability are Provided for Each DT in VARIDT 2.0 (Graphic Illustration) :

α. Mutation-induced Spatial Variations in Folded State (MISVFS)

145 mutation-induced structures originating from 42 DTs

β. Difference among the DT Structures of Human and Model Organisms (DASHMO)

1,622 inter-species structures from 17 species covering 292 DTs

γ. Outward-facing and Inward-facing Conformations (OFAIFC)

118 conformations belonging to 59 DTs

δ. Xenobiotics-driven Alterations in 3D Complex (XEDAIC)

822 xenobiotics-regulated structures of 506 xenobiotics in complex with 57 DTs


Three Aspects of Genenal Variability Data are Provided for Each DT in VARIDT 1.0 (Graphic Illustration) :

α. Epigenetic Regulations and Genetic Polymorphisms of DTs (ERGPDT)

23,947 DNA methylations, 7,225 noncoding RNA regulations, 92 histone modifications and 1,278 genetic polymorphisms of DTs

β. Disease-, Species-, and Tissue-Specific Protein Abundances (DSTSPA)

Differential abundance profiles and downloadable data of 257 DTs in 21,781 patients/healthy individuals of 61 tissues and 108 diseases

Protein abundances of 245 DTs in 67 tissues of Homo sapiens or model organisms (Mus musculus and Rattus norvegicus)

γ. Exogenous Factors Modulating DT Activity (EFMDTA)

1,225 exogenous factors (dietary constituents, small molecular/biological drugs, natural products, etc.) modulating activity of 148 DTs

 

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