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Abstract
We report the production and availability of over 7000 fully sequence verified plasmid ORF clones representing over 3400 unique human genes. These ORF clones were derived using the human MGC collection as template and were produced in two formats: with and without stop codons. Thus, this collection supports the production of either native protein or proteins with fusion tags added to either or both ends. The template clones used to generate this collection were enriched in three ways. First, gene redundancy was removed. Second, clones were selected to represent the best available GenBank reference sequence. Finally, a literature-based software tool was used to evaluate the list of target genes to ensure that it broadly reflected biomedical research interests. The target gene list was compared with 4000 human diseases and over 8500 biological and chemical MeSH classes in ∼15 Million publications recorded in PubMed at the time of analysis. The outcome of this analysis revealed that relative to the genome and the MGC collection, this collection is enriched for the presence of genes with published associations with a wide range of diseases and biomedical terms without displaying a particular bias towards any single disease or concept. Thus, this collection is likely to be a powerful resource for researchers who wish to study protein function in a set of genes with documented biomedical significance.
Highlights
The study of protein function often demands high quality plasmid clones that contain the relevant open reading frames (ORFs) in a format compatible with protein expression
To make the most useful ORF clone set of the Mammalian Gene Collection (MGC) clones, we wished to select an enriched set of genes that is of particular interest to both medicine and biology
The result of this query was compared with queries using either all unique genes represented in MGC or all,33,000 human genes listed at the time in LocusLink (2004, : EntrezGene [15])
Summary
The study of protein function often demands high quality plasmid clones that contain the relevant open reading frames (ORFs) in a format compatible with protein expression. High throughput methods have created the demand for clones that encode a class of proteins of interest or the entire proteome of a species. To avoid erroneous or ambiguous results regarding the expressed proteins, it is important that the plasmids are clonal isolates that are fully sequence verified. For many eukaryotic species, including humans, the number of protein coding sequences exceeds 15,000 genes, making the production of comprehensive sequence-verified ORF clone collections daunting and expensive. One strategy is for researchers to focus on (a) meaningful subset(s) of genes for functional studies relevant to the biological questions they wish to address. For a human ORF collection the criteria for selecting genes are mostly driven by researchers’ interest and clone availability, resulting often in either collections of special interest [4] [5], or more ‘random’ lists of genes in collections (RZPD, Invitrogen)
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