Abstract

The Computational Genomics Research Team will interact with the Functional Genomics Team to develop algorithms for predicting function of coding region variants and for analyzing expression levels and splice variant forms of transporters from RNAseq studies in kidney and liver banks. In addition, they will work together to identify potential regulatory regions of the membrane transporter genes. One of the approaches will be to generate a co-expression network and to construct a transcription network. The group will also expand their previous effort to define substrate specificity of membrane transporters and to develop predictive models for substrate-dependent effects of coding region variants.

  Funding Agency

Agency
National Institute of Health (NIH)
Institute
National Institute of General Medical Sciences (NIGMS)
Type
Research Program--Cooperative Agreements (U19)
Project #
5U19GM061390-13
Application #
8377553
Study Section
Special Emphasis Panel (ZRG1-GGG-M)
Project Start
Project End
Budget Start
2012-07-01
Budget End
2013-06-30
Support Year
13
Fiscal Year
2012
Total Cost
$255,415
Indirect Cost
$61,415

  Institution

Name
University of California San Francisco
Department
Type
DUNS #
094878337
City
San Francisco
State
CA
Country
United States
Zip Code
94143

  Publications

Rotroff, Daniel M; Yee, Sook Wah; Zhou, Kaixin et al. (2018) Genetic Variants in CPA6 and PRPF31 Are Associated With Variation in Response to Metformin in Individuals With Type 2 Diabetes. Diabetes 67:1428-1440
Li, M; Seiser, E L; Baldwin, R M et al. (2018) ABC transporter polymorphisms are associated with irinotecan pharmacokinetics and neutropenia. Pharmacogenomics J 18:35-42
Kim, Kyungpil; Theusch, Elizabeth; Kuang, Yu-Lin et al. (2018) ZNF542P is a pseudogene associated with LDL response to simvastatin treatment. Sci Rep 8:12443
Sá, Ana Caroline C; Webb, Amy; Gong, Yan et al. (2018) Blood pressure signature genes and blood pressure response to thiazide diuretics: results from the PEAR and PEAR-2 studies. BMC Med Genomics 11:55
Singh, Sonal; Wang, Zhiying; Shahin, Mohamed H et al. (2018) Targeted sequencing identifies a missense variant in the BEST3 gene associated with antihypertensive response to hydrochlorothiazide. Pharmacogenet Genomics 28:251-255
Ryu, Ann H; Eckalbar, Walter L; Kreimer, Anat et al. (2017) Use antibiotics in cell culture with caution: genome-wide identification of antibiotic-induced changes in gene expression and regulation. Sci Rep 7:7533
Eclov, Rachel J; Kim, Mee J; Smith, Robin P et al. (2017) In Vivo Hepatic Enhancer Elements in the Human ABCG2 Locus. Drug Metab Dispos 45:208-215
Wu, Hsin-Fang; Hristeva, Nadya; Chang, Jae et al. (2017) Rosuvastatin Pharmacokinetics in Asian and White Subjects Wild Type for Both OATP1B1 and BCRP Under Control and Inhibited Conditions. J Pharm Sci 106:2751-2757
Chhibber, A; French, C E; Yee, S W et al. (2017) Transcriptomic variation of pharmacogenes in multiple human tissues and lymphoblastoid cell lines. Pharmacogenomics J 17:137-145
Wheeler, Heather E; Gamazon, Eric R; Frisina, Robert D et al. (2017) Variants in WFS1 and Other Mendelian Deafness Genes Are Associated with Cisplatin-Associated Ototoxicity. Clin Cancer Res 23:3325-3333

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