The secreted protein discovery initiative (SPDI), a large-scale effort to identify novel human secreted and transmembrane proteins: a bioinformatics assessment.
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Clark HF, Gurney AL, Abaya E, Baker K, Baldwin D, Brush J, Chen J, Chow B, Chui C, Crowley C, Currell B, Deuel B, Dowd P, Eaton D, Foster J, Grimaldi C, Gu Q, Hass PE, Heldens S, Huang A, Kim HS, Klimowski L, Jin Y, Johnson S, Lee J, Lewis L, Liao D, Mark M, Robbie E, Sanchez C, Schoenfeld J, Seshagiri S, Simmons L, Singh J, Smith V, Stinson J, Vagts A, Vandlen R, Watanabe C, Wieand D, Woods K, Xie MH, Yansura D, Yi S, Yu G, Yuan J, Zhang M, Zhang Z, Goddard A, Wood WI, Godowski P, Gray A
The secreted protein discovery initiative (SPDI), a large-scale effort to identify novel human secreted and transmembrane proteins: a bioinformatics assessment.
Genome Res. 2003 Oct;13(10):2265-70. Epub 2003 Sep 15.
- PubMed ID
- 12975309 [ View in PubMed]
- Abstract
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.
DrugBank Data that Cites this Article
- Polypeptides
Name UniProt ID Dehydrogenase/reductase SDR family member 4 Q9BTZ2 Details Toll-like receptor 7 Q9NYK1 Details 3-keto-steroid reductase/17-beta-hydroxysteroid dehydrogenase 7 P56937 Details Protein amnionless Q9BXJ7 Details Albumin P02768 Details Spermine oxidase Q9NWM0 Details Retinol dehydrogenase 13 Q8NBN7 Details Vitamin K epoxide reductase complex subunit 1 Q9BQB6 Details Angiotensin-converting enzyme 2 Q9BYF1 Details Tumor necrosis factor ligand superfamily member 13B Q9Y275 Details Toll-like receptor 9 Q9NR96 Details Endoplasmic reticulum mannosyl-oligosaccharide 1,2-alpha-mannosidase Q9UKM7 Details Heparan sulfate glucosamine 3-O-sulfotransferase 3A1 Q9Y663 Details Cathepsin L2 O60911 Details ADP-ribose pyrophosphatase, mitochondrial Q9BW91 Details Methionine adenosyltransferase 2 subunit beta Q9NZL9 Details Choline transporter-like protein 4 Q53GD3 Details Choline transporter-like protein 3 Q8N4M1 Details Prolyl 4-hydroxylase subunit alpha-2 O15460 Details Beta-1,4-galactosyltransferase 4 O60513 Details Thioredoxin domain-containing protein 12 O95881 Details Probable glutathione peroxidase 8 Q8TED1 Details Glutathione peroxidase 7 Q96SL4 Details Short-chain dehydrogenase/reductase 3 O75911 Details All-trans-retinol 13,14-reductase Q6NUM9 Details Retinol dehydrogenase 14 Q9HBH5 Details Estradiol 17-beta-dehydrogenase 11 Q8NBQ5 Details Dehydrogenase/reductase SDR family member 11 Q6UWP2 Details Phosphopantothenoylcysteine decarboxylase Q96CD2 Details Gamma-secretase subunit APH-1A Q96BI3 Details Platelet-derived growth factor D Q9GZP0 Details Interleukin-23 subunit alpha Q9NPF7 Details Tumor necrosis factor receptor superfamily member 10B O14763 Details Prostate stem cell antigen O43653 Details Transmembrane glycoprotein NMB Q14956 Details SLAM family member 7 Q9NQ25 Details Toll-like receptor 8 Q9NR97 Details Carbonic anhydrase-related protein 10 Q9NS85 Details Carbonic anhydrase-related protein 11 O75493 Details Carbonic anhydrase 14 Q9ULX7 Details Sodium channel regulatory subunit beta-2 O60939 Details Matrix metalloproteinase-27 Q9H306 Details Matrix metalloproteinase-28 Q9H239 Details Pannexin-1 Q96RD7 Details Retinoid-inducible serine carboxypeptidase Q9HB40 Details Lactase-like protein Q6UWM7 Details NADH-cytochrome b5 reductase 1 Q9UHQ9 Details Serine protease inhibitor Kazal-type 6 Q6UWN8 Details L-amino-acid oxidase Q96RQ9 Details Catechol O-methyltransferase domain-containing protein 1 Q86VU5 Details Lactosylceramide alpha-2,3-sialyltransferase Q9UNP4 Details N-acetylmuramoyl-L-alanine amidase Q96PD5 Details Serine/threonine-protein kinase TAO2 Q9UL54 Details A disintegrin and metalloproteinase with thrombospondin motifs 4 O75173 Details Cytochrome P450 4F12 Q9HCS2 Details Solute carrier family 22 member 12 Q96S37 Details Hyaluronan and proteoglycan link protein 3 Q96S86 Details Layilin Q6UX15 Details C-type lectin domain family 14 member A Q86T13 Details Fibroblast growth factor 19 O95750 Details Hephaestin Q9BQS7 Details Peflin Q9UBV8 Details Diacylglycerol O-acyltransferase 2 Q96PD7 Details Protein RIC-3 Q7Z5B4 Details Tachykinin-3 Q9UHF0 Details C-type lectin domain family 4 member E Q9ULY5 Details A disintegrin and metalloproteinase with thrombospondin motifs 13 Q76LX8 Details Receptor-interacting serine/threonine-protein kinase 2 O43353 Details Sclerostin Q9BQB4 Details Hepcidin P81172 Details Receptor for retinol uptake STRA6 Q9BX79 Details Proton-coupled zinc antiporter SLC30A5 Q8TAD4 Details Zinc transporter ZIP9 Q9NUM3 Details Angiopoietin-related protein 3 Q9Y5C1 Details Equilibrative nucleoside transporter 3 Q9BZD2 Details Lymphatic vessel endothelial hyaluronic acid receptor 1 Q9Y5Y7 Details Dipeptidase 3 Q9H4B8 Details CD276 antigen Q5ZPR3 Details