Exploring protein domain organization by recognition of secondary structure packing interfaces

Deng, Lizong; Wu, Aiping; Dai, Wentao; Song, Tingrui; Cui, Ya; Jiang, Taijiao

doi:10.1093/bioinformatics/btu327

Cited by 1 publication

(1 citation statement)

References 35 publications

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“…Since domains are the basic functional units of proteins (Deng et al, 2014), we identified domains in SPs. We scanned the SPs using InterPorScan (Jones et al, 2014) (version 57) based on eleven integrative protein family databases, including Pfam, CATH-Gene3D, PIRSF, PROSITE, HAMAP, PRINTS, ProDom, SMART, TIGRFAMs, SUPERFAMILY, and PANTHER.…”

Section: Resultsmentioning

confidence: 99%

Comprehensive Identification and Characterization of Human Secretome Based on Integrative Proteomic and Transcriptomic Data

Chen

Liu

et al. 2019

Front. Cell Dev. Biol.

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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.

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Section: Resultsmentioning

confidence: 99%