Protease target prediction via matrix factorization

Bioinformatics
Simone MariniTatsuya Akutsu

Abstract

Protein cleavage is an important cellular event, involved in a myriad of processes, from apoptosis to immune response. Bioinformatics provides in silico tools, such as machine learning-based models, to guide the discovery of targets for the proteases responsible for protein cleavage. State-of-the-art models have a scope limited to specific protease families (such as Caspases), and do not explicitly include biological or medical knowledge (such as the hierarchical protein domain similarity or gene-gene interactions). To fill this gap, we present a novel approach for protease target prediction based on data integration. By representing protease-protein target information in the form of relational matrices, we design a model (i) that is general and not limited to a single protease family, and (b) leverages on the available knowledge, managing extremely sparse data from heterogeneous data sources, including primary sequence, pathways, domains and interactions. When compared with other algorithms on test data, our approach provides a better performance even for models specifically focusing on a single protease family. https://gitlab.com/smarini/MaDDA/ (Matlab code and utilized data.). Supplementary data are available at Bioinformati...Continue Reading

References

Aug 28, 1998·Phytochemistry·P B Barrett, J L Harwood
Mar 23, 2004·Bioinformatics·Michael A GilchristAndreas Wagner
Aug 19, 2005·Journal of Bioinformatics and Computational Biology·Sarah E BoydMaria Garcia de la Banda
Dec 19, 2006·FEBS Letters·Jerzy OrlowskiPiotr Zielenkiewicz
Oct 5, 2007·Nucleic Acids Research·Balaji RaghavachariRaja Jothi
Apr 3, 2008·Hematological Oncology·H Dean HosgoodQing Lan
Aug 1, 2008·Arthritis and Rheumatism·Eugene Y ZhenKevin L Duffin
Dec 9, 2008·Lung Cancer : Journal of the International Association for the Study of Lung Cancer·Won Kee LeeJae Yong Park
Mar 28, 2009·The Biochemical Journal·Laure GibotCatherine Le Jossic-Corcos
Feb 5, 2010·Bioinformatics·Jiangning SongJames C Whisstock
May 28, 2010·Bioinformatics·David T BarkanAndrej Sali
Aug 11, 2011·Current Protein & Peptide Science·Simone MariniQiang Yang
Mar 28, 2012·The Journal of Biological Chemistry·Diana BarthelPeter F Zipfel
Jul 12, 2013·Bioinformatics·Joan Planas-IglesiasBaldo Oliva
Oct 2, 2013·Nucleic Acids Research·Roberto MoscaPatrick Aloy
Oct 24, 2013·Bioinformatics·Mingjun WangJiangning Song
Nov 28, 2014·Nucleic Acids Research·UNKNOWN Gene Ontology Consortium
Sep 10, 2015·IEEE Transactions on Pattern Analysis and Machine Intelligence·Marinka Zitnik, Blaz Zupan
Nov 4, 2015·Nucleic Acids Research·Neil D RawlingsRobert Finn
Dec 17, 2015·Bioinformatics·Vladimir GligorijevićNataša Pržulj
Nov 1, 2016·Nature Medicine·Xiaohui ZhaoKaren H Ashe
Dec 3, 2016·Nucleic Acids Research·Robert D FinnAlex L Mitchell
Dec 3, 2016·Nucleic Acids Research·Minoru KanehisaKanae Morishima
Dec 8, 2016·Nucleic Acids Research·Damian SzklarczykChristian von Mering
Dec 17, 2016·Nucleic Acids Research·Andrew Chatr-AryamontriMike Tyers

❮ Previous
Next ❯

Citations

Jun 12, 2019·PloS One·Andrej ČoparMarinka Zitnik
Oct 28, 2019·Frontiers in Genetics·Nelson NazzicariSimone Marini
Feb 26, 2021·BioMed Research International·Yihua YeXiaochen Bo

❮ Previous
Next ❯

Related Concepts

Related Feeds

Apoptosis

Apoptosis is a specific process that leads to programmed cell death through the activation of an evolutionary conserved intracellular pathway leading to pathognomic cellular changes distinct from cellular necrosis

Apoptotic Caspases

Apoptotic caspases belong to the protease enzyme family and are known to play an essential role in inflammation and programmed cell death. Here is the latest research.