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Pubmed ID :12975309
Publication Date : //

The secreted protein discovery initiative (SPDI), a large-scale effort to identify novel human secreted and transmembrane proteins: a bioinformatics assessment.


A large-scale effort, termed the Secreted Protein Discovery Initiative (SPDI), was undertaken to identify novel secreted and transmembrane proteins. In the first of several approaches, a biological signal sequence trap in yeast cells was utilized to identify cDNA clones encoding putative secreted proteins. A second strategy utilized various algorithms that recognize features such as the hydrophobic properties of signal sequences to identify putative proteins encoded by expressed sequence tags (ESTs) from human cDNA libraries. A third approach surveyed ESTs for protein sequence similarity to a set of known receptors and their ligands with the BLAST algorithm. Finally, both signal-sequence prediction algorithms and BLAST were used to identify single exons of potential genes from within human genomic sequence. The isolation of full-length cDNA clones for each of these candidate genes resulted in the identification of >1000 novel proteins. A total of 256 of these cDNAs are still novel, including variants and novel genes, per the most recent GenBank release version. The success of this large-scale effort was assessed by a bioinformatics analysis of the proteins through predictions of protein domains, subcellular localizations, and possible functional roles. The SPDI collection should facilitate efforts to better understand intercellular communication, may lead to new understandings of human diseases, and provides potential opportunities for the development of therapeutics.

Authors : Clark Hilary F , Gurney Austin L , Abaya Evangeline , Baker Kevin , Baldwin Daryl , Brush Jennifer , Chen Jian , Chow Bernard , Chui Clarissa , Crowley Craig , Currell Bridget , Deuel Bethanne , Dowd Patrick , Eaton Dan , Foster Jessica , Grimaldi Christopher , Gu Qimin , Hass Philip E , Heldens Sherry , Huang Arthur , Kim Hok Seon , Klimowski Laura , Jin Yisheng , Johnson Stephanie , Lee James , Lewis Lhney , Liao Dongzhou , Mark Melanie , Robbie Edward , Sanchez Celina , Schoenfeld Jill , Seshagiri Somasekar , Simmons Laura , Singh Jennifer , Smith Victoria , Stinson Jeremy , Vagts Alicia , Vandlen Richard , Watanabe Colin , Wieand David , Woods Kathryn , Xie Ming-Hong , Yansura Daniel , Yi Sothy , Yu Guoying , Yuan Jean , Zhang Min , Zhang Zemin , Goddard Audrey , Wood William I , Godowski Paul , Gray Alane ,

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