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

Article Details

Citation

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
NameUniProt ID
Dehydrogenase/reductase SDR family member 4Q9BTZ2Details
Toll-like receptor 7Q9NYK1Details
3-keto-steroid reductaseP56937Details
Protein amnionlessQ9BXJ7Details
Serum albuminP02768Details
Spermine oxidaseQ9NWM0Details
Retinol dehydrogenase 13Q8NBN7Details
Vitamin K epoxide reductase complex subunit 1Q9BQB6Details
Angiotensin-converting enzyme 2Q9BYF1Details
Tumor necrosis factor ligand superfamily member 13BQ9Y275Details
Toll-like receptor 9Q9NR96Details
Endoplasmic reticulum mannosyl-oligosaccharide 1,2-alpha-mannosidaseQ9UKM7Details
Heparan sulfate glucosamine 3-O-sulfotransferase 3A1Q9Y663Details
Cathepsin L2O60911Details
ADP-ribose pyrophosphatase, mitochondrialQ9BW91Details
Methionine adenosyltransferase 2 subunit betaQ9NZL9Details
Choline transporter-like protein 4Q53GD3Details
Choline transporter-like protein 3Q8N4M1Details
Prolyl 4-hydroxylase subunit alpha-2O15460Details
Beta-1,4-galactosyltransferase 4O60513Details
Thioredoxin domain-containing protein 12O95881Details
Probable glutathione peroxidase 8Q8TED1Details
Glutathione peroxidase 7Q96SL4Details
Short-chain dehydrogenase/reductase 3O75911Details
All-trans-retinol 13,14-reductaseQ6NUM9Details
Retinol dehydrogenase 14Q9HBH5Details
Estradiol 17-beta-dehydrogenase 11Q8NBQ5Details
Dehydrogenase/reductase SDR family member 11Q6UWP2Details
Phosphopantothenoylcysteine decarboxylaseQ96CD2Details
Gamma-secretase subunit APH-1AQ96BI3Details
Platelet-derived growth factor DQ9GZP0Details
Interleukin-23 subunit alphaQ9NPF7Details
Tumor necrosis factor receptor superfamily member 10BO14763Details
Prostate stem cell antigenO43653Details
Transmembrane glycoprotein NMBQ14956Details
SLAM family member 7Q9NQ25Details
Toll-like receptor 8Q9NR97Details
Carbonic anhydrase-related protein 10Q9NS85Details
Carbonic anhydrase-related protein 11O75493Details
Carbonic anhydrase 14Q9ULX7Details
Sodium channel subunit beta-2O60939Details
Matrix metalloproteinase-27Q9H306Details
Matrix metalloproteinase-28Q9H239Details
Pannexin-1Q96RD7Details
Retinoid-inducible serine carboxypeptidaseQ9HB40Details
Lactase-like proteinQ6UWM7Details
NADH-cytochrome b5 reductase 1Q9UHQ9Details
Serine protease inhibitor Kazal-type 6Q6UWN8Details
L-amino-acid oxidaseQ96RQ9Details
Catechol O-methyltransferase domain-containing protein 1Q86VU5Details
Lactosylceramide alpha-2,3-sialyltransferaseQ9UNP4Details
N-acetylmuramoyl-L-alanine amidaseQ96PD5Details
Serine/threonine-protein kinase TAO2Q9UL54Details
A disintegrin and metalloproteinase with thrombospondin motifs 4O75173Details
Cytochrome P450 4F12Q9HCS2Details
Solute carrier family 22 member 12Q96S37Details
Hyaluronan and proteoglycan link protein 3Q96S86Details
LayilinQ6UX15Details
C-type lectin domain family 14 member AQ86T13Details
Fibroblast growth factor 19O95750Details
HephaestinQ9BQS7Details
PeflinQ9UBV8Details
Diacylglycerol O-acyltransferase 2Q96PD7Details
Protein RIC-3Q7Z5B4Details
Tachykinin-3Q9UHF0Details
C-type lectin domain family 4 member EQ9ULY5Details
A disintegrin and metalloproteinase with thrombospondin motifs 13Q76LX8Details
Receptor-interacting serine/threonine-protein kinase 2O43353Details
SclerostinQ9BQB4Details
HepcidinP81172Details
Receptor for retinol uptake STRA6Q9BX79Details
Zinc transporter 5Q8TAD4Details
Zinc transporter ZIP9Q9NUM3Details
Angiopoietin-related protein 3Q9Y5C1Details
Equilibrative nucleoside transporter 3Q9BZD2Details
Lymphatic vessel endothelial hyaluronic acid receptor 1Q9Y5Y7Details
Dipeptidase 3Q9H4B8Details