Network‑based gene function inference method to predict optimal gene functions associated with fetal growth restriction

Molecular Medicine Reports
Ke-Jun YeMeng-Jia Peng

Abstract

The guilt by association (GBA) principle has been widely used to predict gene functions, and a network‑based approach may enhance the confidence and stability of the analysis compared with focusing on individual genes. Fetal growth restriction (FGR), is the second primary cause of perinatal mortality. Therefore, the present study aimed to predict the optimal gene functions for FGR using a network‑based GBA method. The method was comprised of four parts: Identification of differentially‑expressed genes (DEGs) between patients with FGR and normal controls based on gene expression data; construction of a co‑expression network (CEN) dependent on DEGs, using the Spearman correlation coefficient algorithm; collection of gene ontology (GO) data on the basis of a known confirmed database and DEGs; and prediction of optimal gene functions using the GBA algorithm, for which the area under the receiver operating characteristic curve (AUC) was obtained for each GO term. A total of 115 DEGs and 109 GO terms were obtained for subsequent analysis. All DEGs were mapped to the CEN and formed 6,555 edges. The results of GBA algorithm demonstrated that 78 GO terms had a good classification performance with AUC >0.5. In particular, the AUC for 5 o...Continue Reading

References

Feb 13, 2003·Nucleic Acids Research·Rafael A IrizarryTerence P Speed
May 2, 2006·Statistical Applications in Genetics and Molecular Biology·Bin Zhang, Steve Horvath
Jan 26, 2007·BMC Bioinformatics·Andy M Yip, Steve Horvath
Oct 5, 2007·The Journal of Neuroscience : the Official Journal of the Society for Neuroscience·Stephen E P SmithPaul H Patterson
Jul 22, 2008·Genome Biology·Lourdes Peña-CastilloFrederick P Roth
Aug 16, 2008·PLoS Computational Biology·Steve Horvath, Jun Dong
Jul 30, 2010·Proceedings of the National Academy of Sciences of the United States of America·Elizabeth A GriceJulia A Segre
Mar 3, 2011·PloS One·Jesse Gillis, Paul Pavlidis
May 10, 2011·Bioinformatics·Jesse Gillis, Paul Pavlidis
Aug 4, 2011·Reproductive Biology and Endocrinology : RB&E·Haruki NishizawaYasuhiro Udagawa
Mar 1, 2012·IET Systems Biology·Z-P LiuL Chen
Mar 8, 2012·Nature Medicine·Olivia Osborn, Jerrold M Olefsky
Apr 25, 2012·Archives of Gynecology and Obstetrics·Luciano Marcondes Machado NardozzaAntonio Fernandes Moron
Aug 29, 2012·Annals of Oncology : Official Journal of the European Society for Medical Oncology·O J Finn
Jan 30, 2014·Angewandte Chemie·Christoph FenzlOtto S Wolfbeis
Nov 28, 2014·Nucleic Acids Research·UNKNOWN Gene Ontology Consortium
Jan 22, 2015·Nucleic Acids Research·Matthew E RitchieGordon K Smyth

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