Improving protein function prediction using protein sequence and GO-term similarities

Bioinformatics
Stavros MakrodimitrisMarcel J T Reinders

Abstract

Most automatic functional annotation methods assign Gene Ontology (GO) terms to proteins based on annotations of highly similar proteins. We advocate that proteins that are less similar are still informative. Also, despite their simplicity and structure, GO terms seem to be hard for computers to learn, in particular the Biological Process ontology, which has the most terms (>29 000). We propose to use Label-Space Dimensionality Reduction (LSDR) techniques to exploit the redundancy of GO terms and transform them into a more compact latent representation that is easier to predict. We compare proteins using a sequence similarity profile (SSP) to a set of annotated training proteins. We introduce two new LSDR methods, one based on the structure of the GO, and one based on semantic similarity of terms. We show that these LSDR methods, as well as three existing ones, improve the Critical Assessment of Functional Annotation performance of several function prediction algorithms. Cross-validation experiments on Arabidopsis thaliana proteins pinpoint the superiority of our GO-aware LSDR over generic LSDR. Our experiments on A.thaliana proteins show that the SSP representation in combination with a kNN classifier outperforms state-of-the-...Continue Reading

References

Feb 26, 2004·Journal of Computational Biology : a Journal of Computational Molecular Cell Biology·Li Liao, William Stafford Noble
Feb 1, 2005·Trends in Genetics : TIG·Steven Lockton, Brandon S Gaut
Jun 16, 2005·Bioinformatics·Purvesh KhatriSorin Draghici
Feb 12, 2008·Bioinformatics·Mark N Wass, Michael J E Sternberg
May 19, 2009·BMC Bioinformatics·Nazar ZakiPiers Campbell
Aug 4, 2009·PLoS Computational Biology·Catia PesquitaFrancisco M Couto
Mar 3, 2010·PloS One·Yiannis A I KourmpetisCajo J F ter Braak
Nov 16, 2011·IEEE/ACM Transactions on Computational Biology and Bioinformatics·Xiao-Fei Zhang, Dao-Qing Dai
May 19, 2012·Neural Computation·Farbound Tai, Hsuan-Tien Lin
May 30, 2012·Nucleic Acids Research·Mark N WassMichael J E Sternberg
Oct 26, 2012·BMC Bioinformatics·Riccardo BellazziPaolo Romano
Jan 29, 2013·Nature Methods·Predrag RadivojacIddo Friedberg
Mar 27, 2013·BMC Bioinformatics·Liang LanSlobodan Vucetic
Jul 3, 2013·Bioinformatics·Wyatt T Clark, Predrag Radivojac
Jul 1, 2013·Journal of Advanced Research·Indu SainiArun Khosla
Jun 13, 2015·BioMed Research International·Xin-Fang LeongKamsiah Jaarin
Aug 19, 2015·Methods : a Companion to Methods in Enzymology·Qingtian GongWeidong Tian
Sep 10, 2015·IEEE Transactions on Pattern Analysis and Machine Intelligence·Marinka Zitnik, Blaz Zupan
Sep 18, 2015·GigaScience·Indika KahandaAsa Ben-Hur
Feb 6, 2017·BMC Systems Biology·Guoxian YuJun Wang
Feb 15, 2017·Journal of Biomedical Semantics·Maxat Kulmanov, Robert Hoehndorf
Oct 17, 2017·Computational Biology and Chemistry·Guoxian YuJun Wang

❮ Previous
Next ❯

Citations

Oct 12, 2019·Proteins·Rosalin Bonetta, Gianluca Valentino
May 12, 2020·Frontiers in Genetics·Yingwen ZhaoGuoxian Yu
Nov 13, 2020·Database : the Journal of Biological Databases and Curation·Carlota CardosoCatia Pesquita
Oct 31, 2020·Genes·Stavros MakrodimitrisMarcel J T Reinders

❮ Previous
Next ❯

Software Mentioned

Knowledge
kNN
SD
TRANSFERBLAST
PLST
MS
No
SEM
SSP
CAFA

Related Concepts

Trending Feeds

COVID-19

Coronaviruses encompass a large family of viruses that cause the common cold as well as more serious diseases, such as the ongoing outbreak of coronavirus disease 2019 (COVID-19; formally known as 2019-nCoV). Coronaviruses can spread from animals to humans; symptoms include fever, cough, shortness of breath, and breathing difficulties; in more severe cases, infection can lead to death. This feed covers recent research on COVID-19.

Blastomycosis

Blastomycosis fungal infections spread through inhaling Blastomyces dermatitidis spores. Discover the latest research on blastomycosis fungal infections here.

Nuclear Pore Complex in ALS/FTD

Alterations in nucleocytoplasmic transport, controlled by the nuclear pore complex, may be involved in the pathomechanism underlying multiple neurodegenerative diseases including Amyotrophic Lateral Sclerosis and Frontotemporal Dementia. Here is the latest research on the nuclear pore complex in ALS and FTD.

Applications of Molecular Barcoding

The concept of molecular barcoding is that each original DNA or RNA molecule is attached to a unique sequence barcode. Sequence reads having different barcodes represent different original molecules, while sequence reads having the same barcode are results of PCR duplication from one original molecule. Discover the latest research on molecular barcoding here.

Chronic Fatigue Syndrome

Chronic fatigue syndrome is a disease characterized by unexplained disabling fatigue; the pathology of which is incompletely understood. Discover the latest research on chronic fatigue syndrome here.

Evolution of Pluripotency

Pluripotency refers to the ability of a cell to develop into three primary germ cell layers of the embryo. This feed focuses on the mechanisms that underlie the evolution of pluripotency. Here is the latest research.

Position Effect Variegation

Position Effect Variagation occurs when a gene is inactivated due to its positioning near heterochromatic regions within a chromosome. Discover the latest research on Position Effect Variagation here.

STING Receptor Agonists

Stimulator of IFN genes (STING) are a group of transmembrane proteins that are involved in the induction of type I interferon that is important in the innate immune response. The stimulation of STING has been an active area of research in the treatment of cancer and infectious diseases. Here is the latest research on STING receptor agonists.

Microbicide

Microbicides are products that can be applied to vaginal or rectal mucosal surfaces with the goal of preventing, or at least significantly reducing, the transmission of sexually transmitted infections. Here is the latest research on microbicides.