The secreted protein discovery initiative (SPDI), a large-scale effort to identify novel human secreted and transmembrane proteins: a bioinformatics assessment.
By H. Clark, A. Gurney, Evangeline Abaya, K. Baker, D. Baldwin, Jennifer Brush, Jian Chen, B. Chow, C. Chui, C. Crowley and 42 more. Genome Research, 2003
363 citations recorded by the source corpus.
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.
Subfields: Molecular Biology
View Paper: https://www.semanticscholar.org/paper/6fcdd103cb31627d5d93d6a065b68afa42dff162
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In Molecular Biology
Citations in the corpus
- The surface protein TIGIT suppresses T cell activation by promoting the generation of mature immunoregulatory dendritic cells (2009, background): “PVR is a high-affinity receptor for TIGIT To identify binding partners of TIGIT, we screened a large library of secreted protein”
- Control of matrix metalloproteinase catalytic activity. (2007, background): “§ In addition to being identified in a large scale bioinformatic search of secreted proteins (Clark et al., 2003), full-length cDNAs for human, rat, and northern tree shrew MMP-27 have been submitted to GenBank (access no.”