ArticleAAPS pharmSci2003
A semiautomated approach to gene discovery through expressed sequence tag data mining: discovery of new human transporter genes.
Article in AAPS pharmSci, 2003. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 5 papers.
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Who cites it
5 citing papers in PubMed.
- Energy coupling mechanisms of MFS transporters.Protein science : a publication of the Protein Society · 2015Review
- Structure of the YajR transporter suggests a transport mechanism based on the conserved motif A.Proceedings of the National Academy of Sciences of the United States of America · 2013Article
- Sialin (SLC17A5) functions as a nitrate transporter in the plasma membrane.Proceedings of the National Academy of Sciences of the United States of America · 2012Article
- Validation of an NSP-based (negative selection pattern) gene family identification strategy.BMC bioinformatics · 2008Article
- Messenger RNA expression of transporter and ion channel genes in undifferentiated and differentiated Caco-2 cells compared to human intestines.Pharmaceutical research · 2003Article
Corrections and comments
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Authors and funding
4 authors.
Funding
Abstract
Identification and functional characterization of the genes in the human genome remain a major challenge. A principal source of publicly available information used for this purpose is the National Center for Biotechnology Information database of expressed sequence tags (dbEST), which contains over 4 million human ESTs. To extract the information buried in this data more effectively, we have developed a semiautomated method to mine dbEST for uncharacterized human genes. Starting with a single protein input sequence, a family of related proteins from all species is compiled. This entire family is then used to mine the human EST database for new gene candidates. Evaluation of putative new gene candidates in the context of a family of characterized proteins provides a framework for inference of the structure and function of the new genes. When applied to a test data set of 28 families within the major facilitator superfamily (MFS) of membrane transporters, our protocol found 73 previously characterized human MFS genes and 43 new MFS gene candidates. Development of this approach provided insights into the problems and pitfalls of automated data mining using public databases.
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Registered trials
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