Computationally predicting protein-RNA interactions using only positive and unlabeled examples

Journal of Bioinformatics and Computational Biology
Zhanzhan ChengJihong Guan

Abstract

Protein-RNA interactions (PRIs) are considerably important in a wide variety of cellular processes, ranging from transcriptional and post-transcriptional regulations of gene expression to the active defense of host against virus. With the development of high throughput technology, large amounts of PRI information is available for computationally predicting unknown PRIs. In recent years, a number of computational methods for predicting PRIs have been developed in the literature, which usually artificially construct negative samples based on verified nonredundant datasets of PRIs to train classifiers. However, such negative samples are not real negative samples, some even may be unknown positive samples. Consequently, the classifiers trained with such training datasets cannot achieve satisfactory prediction performance. In this paper, we propose a novel method PRIPU that employs biased-support vector machine (SVM) for predicting Protein-RNA Interactions using only Positive and Unlabeled examples. To the best of our knowledge, this is the first work that predicts PRIs using only positive and unlabeled samples. We first collect known PRIs as our benchmark datasets and extract sequence-based features to represent each PRI. To reduce...Continue Reading

References

Apr 1, 1992·Trends in Biochemical Sciences·D Moras
Jun 1, 1997·Current Opinion in Genetics & Development·H Siomi, G Dreyfuss
Jun 30, 1998·Trends in Biochemical Sciences·V Ramakrishnan, S W White
Jul 1, 1998·Annual Review of Biophysics and Biomolecular Structure·P B Moore
Oct 6, 1998·Annual Review of Biochemistry·D N Frank, N R Pace
Jun 9, 1999·Nature Structural Biology·T Hermann, E Westhof
Dec 11, 1999·Nucleic Acids Research·H M BermanP E Bourne
Feb 13, 2001·Nucleic Acids Research·S JonesJ M Thornton
Jun 28, 2002·Cancer Cell·Dinesh SinghWilliam R Sellers
Jul 20, 2002·Current Opinion in Structural Biology·Kathleen B Hall
Dec 2, 2004·Nature Reviews. Molecular Cell Biology·Bin TianMichael B Mathews
Aug 2, 2005·Trends in Biochemical Sciences·Juan MataJürg Bähler
Jun 23, 2006·RNA·Michael TerribiliniDrena Dobbs
Sep 20, 2006·Nucleic Acids Research·Sigrid D AuweterFrédéric H-T Allain
Dec 23, 2006·Proteins·Jonathan J EllisSusan Jones
Mar 16, 2007·Proceedings of the National Academy of Sciences of the United States of America·Juwen ShenHualiang Jiang
Mar 29, 2008·Methods in Molecular Biology·Timothy E BaroniScott A Tenenbaum
Apr 2, 2009·BMB Reports·Mee Young KimSunjoo Jeong
Jul 10, 2009·Methods in Molecular Biology·Alice Barkan
Feb 13, 2010·Journal of Biomedicine & Biotechnology·Almudena Pacheco, Encarnacion Martinez-Salas
Apr 27, 2010·Current Opinion in Structural Biology·Ebru KaymakSean P Ryder
Nov 13, 2010·Nucleic Acids Research·Benjamin A LewisDrena Dobbs
Apr 5, 2011·Nucleic Acids Research·Vera Pancaldi, Jürg Bähler
Dec 24, 2011·BMC Bioinformatics·Usha K MuppiralaDrena Dobbs
Apr 3, 2012·Bioinformatics·Penghao WangJean Yee Hwa Yang
Nov 10, 2012·Molecular BioSystems·Ying WangLuonan Chen

❮ Previous
Next ❯

Citations

Nov 6, 2015·International Journal of Molecular Sciences·Jingna SiRongling Wu
Jun 5, 2015·Briefings in Bioinformatics·Fabrizio FerrèManuela Helmer-Citterich
May 16, 2015·Journal of Bioinformatics and Computational Biology·Xiao-Li Li, Jie Zheng
Dec 21, 2016·Bioinformatics·Xiaoli Zhang, Shiyong Liu
May 9, 2019·Wiley Interdisciplinary Reviews. RNA·Xiaoyong PanHong-Bin Shen
Jun 20, 2019·Protein and Peptide Letters·Amit Sagar, Bin Xue
Apr 28, 2017·Briefings in Bioinformatics·Yuwei ZhangQi Liao
Apr 1, 2017·BMC Systems Biology·Zhanzhan ChengShuigeng Zhou
Mar 22, 2018·Frontiers in Molecular Biosciences·Andrea Cipriano, Monica Ballarino
Feb 25, 2020·Genomics·Mahsa Torkamanian-AfsharAli Masoudi-Nejad
Nov 4, 2021·Briefings in Bioinformatics·Fuyi LiJiangning Song

❮ Previous
Next ❯

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.