ABSTRACT
Secreted proteins (SPs) play important roles in diverse important biological processes; however, a comprehensive and high-quality list of human SPs is still lacking. Here we identified 6,943 high-confidence human SPs (3,522 of them are novel) based on 330,427 human proteins derived from databases of UniProt, Ensembl, AceView, and RefSeq. Notably, 6,267 of 6,943 (90.3%) SPs have the supporting evidences from a large amount of mass spectrometry (MS) and RNA-seq data. We found that the SPs were broadly expressed in diverse tissues as well as human body fluid, and a significant portion of them exhibited tissue-specific expression. Moreover, 14 cancer-specific SPs that their expression levels were significantly associated with the patients' survival of eight different tumors were identified, which could be potential prognostic biomarkers. Strikingly, 89.21% of 6,943 SPs (2,927 novel SPs) contain known protein domains. Those novel SPs we mainly enriched with the known domains regarding immunity, such as Immunoglobulin V-set and C1-set domain. Specifically, we constructed a user-friendly and freely accessible database, SPRomeDB (www.unimd.org/SPRomeDB), to catalog those SPs. Our comprehensive SP identification and characterization gain insights into human secretome and provide valuable resource for future researches.
ABSTRACT
Millions of human single nucleotide polymorphisms (SNPs) or mutations have been identified so far, and these variants could be strongly correlated with phenotypic variations of traits/diseases. Among these variants, non-synonymous ones can result in amino-acid changes that are called single amino-acid polymorphisms (SAPs). Although some studies have tried to investigate the SAPs, only a small fraction of SAPs have been identified due to inadequately inferred protein variation database and the low coverage of mass spectrometry (MS) experiments. Here, we present the dbSAP database for conveniently accessing the comprehensive information and relationships of spectra, peptides and proteins of SAPs, as well as related genes, pathways, diseases and drug targets. In order to fully explore human SAPs, we built a customized protein database that contained comprehensive variant proteins by integrating and annotating the human SNPs and mutations from eight distinct databases (UniProt, Protein Mutation Database, HPMD, MSIPI, MS-CanProVar, dbSNP, Ensembl and COSMIC). After a series of quality controls, a total of 16 854 SAP peptides involving in 439 537 spectra were identified with large scale MS datasets from various human tissues and cell lines. dbSAP is freely available at http://www.megabionet.org/dbSAP/index.html.
Subject(s)
Amino Acid Substitution , Computational Biology/methods , Databases, Protein , Polymorphism, Single Nucleotide , Proteins/genetics , Genetic Variation , Humans , Peptides/chemistry , Peptides/genetics , Proteins/chemistry , Search Engine , Software , Web BrowserABSTRACT
OBJECTIVE: To evaluate the clinical efficacy of alpha-1 A adrenoceptor antagonist (tamsulosin) in the treatment of benign prostatic hyperplasia (BPH) patients with acute urinary retention. METHODS: Seventy-two BPH patients with acute retention of urine were randomly divided into treatment group and control group of 36 patients each. All the patients were treated with indwelling catheter, oral antibiotics and the patients in treatment group tamsulosin 0.4 mg once a day for 3 days. The catheter was removed after 72 hours of treatment. RESULTS: After removal of the catheter, 44% (32/72) of patients voided successfully. The effect rates were 61% (22/36) in the tamsulosin treatment group and 28% (10/36) in the control group(P < 0.01). CONCLUSIONS: Treatment with tamsulosin was effective in raising the success rate of voiding without catheter after an episode of acute urinary retention. The efficacy of treatment was not influenced by the volume of prostate.
