TY - JOUR
T1 - Comprehensive Identification and Characterization of Human Secretome Based on Integrative Proteomic and Transcriptomic Data
AU - Chen, Geng
AU - Chen, Jiwei
AU - Liu, Huanlong
AU - Chen, Shuangguan
AU - Zhang, Yang
AU - Li, Peng
AU - Thierry-Mieg, Danielle
AU - Thierry-Mieg, Jean
AU - Mattes, William
AU - Ning, Baitang
AU - Shi, Tieliu
N1 - Publisher Copyright:
© Copyright © 2019 Chen, Chen, Liu, Chen, Zhang, Li, Thierry-Mieg, Thierry-Mieg, Mattes, Ning and Shi.
PY - 2019/11/21
Y1 - 2019/11/21
N2 - 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.
AB - 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.
KW - RNA-seq
KW - human secretome
KW - proteome
KW - secreted proteins
KW - transcriptome
UR - https://www.scopus.com/pages/publications/85076681333
U2 - 10.3389/fcell.2019.00299
DO - 10.3389/fcell.2019.00299
M3 - 文章
AN - SCOPUS:85076681333
SN - 2296-634X
VL - 7
JO - Frontiers in Cell and Developmental Biology
JF - Frontiers in Cell and Developmental Biology
M1 - 299
ER -
