title: Discovery of new candidate genes related to brain development using protein interaction information.
abstract: Human brain development is a dramatic process composed of a series of complex and fine-tuned spatiotemporal gene expressions. A good comprehension of this process can assist us in developing the potential of our brain. However, we have only limited knowledge about the genes and gene functions that are involved in this biological process. Therefore, a substantial demand remains to discover new brain development-related genes and identify their biological functions. In this study, we aimed to discover new brain-development related genes by building a computational method. We referred to a series of computational methods used to discover new disease-related genes and developed a similar method. In this method, the shortest path algorithm was executed on a weighted graph that was constructed using protein-protein interactions. New candidate genes fell on at least one of the shortest paths connecting two known genes that are related to brain development. A randomization test was then adopted to filter positive discoveries. Of the final identified genes, several have been reported to be associated with brain development, indicating the effectiveness of the method, whereas several of the others may have potential roles in brain development.
authors: College of Information Engineering, Shanghai Maritime University, Shanghai 201306, People's Republic of China.
authors: Lei
authors: L
authors: Chen
authors: Institute of Biochemistry and Cell Biology, Shanghai Institutes for Biological Sciences, Chinese Academy of Sciences, Shanghai 200031, People's Republic of China.
authors: Chen
authors: C
authors: Chu
authors: Institute of Health Sciences, Shanghai Institutes for Biological Sciences, Chinese Academy of Sciences, Shanghai 200025, People's Republic of China.
authors: Xiangyin
authors: X
authors: Kong
authors: Institute of Health Sciences, Shanghai Institutes for Biological Sciences, Chinese Academy of Sciences, Shanghai 200025, People's Republic of China.
authors: Tao
authors: T
authors: Huang
authors: Institute of Systems Biology, Shanghai University, Shanghai 200444, People's Republic of China.
authors: Yu-Dong
authors: YD
authors: Cai
mesh_terms: D001921:Brain / Q000254:growth & development* / Q000378:metabolism*; D001927:Brain Diseases / Q000235:genetics; D018507:Gene Expression Regulation, Developmental; D063990:Gene Ontology; D056726:Genetic Association Studies; D006801:Humans; D060066:Protein Interaction Maps / Q000235:genetics*
references: Gene Expr Patterns. 2005 Feb;5(3):445-51
references: 15661652
references: Proc Natl Acad Sci U S A. 2014 Jan 28;111(4):1355-60
references: 24474760
references: Front Genet. 2014 May 16;5:137
references: 24904637
references: Comput Biol Med. 2010 Mar;40(3):300-5
references: 20089249
references: Peptides. 1985 Mar-Apr;6(2):193-8
references: 4034410
references: Bioinformatics. 2010 Nov 15;26(22):2924-6
references: 20861032
references: Dev Cell. 2008 Dec;15(6):841-53
references: 19081073
references: Endocrinology. 1995 Oct;136(10):4721-4
references: 7664697
references: Front Genet. 2014 May 26;5:143
references: 24904643
references: Trends Neurosci. 2005 Nov;28(11):583-8
references: 16139372
references: Nucleic Acids Res. 2009 Jan;37(Database issue):D412-6
references: 18940858
references: PLoS One. 2012;7(9):e45944
references: 23029334
references: IEEE/ACM Trans Comput Biol Bioinform. 2010 Apr-Jun;7(2):208-17
references: 20431141
references: Mol Biosyst. 2014 Apr;10(4):868-77
references: 24492783
references: PLoS One. 2012;7(4):e35254
references: 22514724
references: Cell Mol Life Sci. 2006 Jul;63(14):1597-613
references: 16699809
references: Mol Biosyst. 2013 Nov;9(11):2720-8
references: 24056857
references: Front Biosci. 2007;12:492-506
references: 17127312
references: Science. 2008 Nov 7;322(5903):881-8
references: 18988837
references: Int J Dev Neurosci. 2002 Oct;20(6):503-10
references: 12392754
references: EMBO J. 2007 Feb 21;26(4):1045-54
references: 17290221
references: Stem Cells Transl Med. 2014 May;3(5):662-70
references: 24692587
references: J Neuroimmune Pharmacol. 2012 Dec;7(4):788-807
references: 23160851
references: Biochem Biophys Res Commun. 2011 Jul 29;411(2):360-4
references: 21741365
references: Gene Expr Patterns. 2014 May;15(1):31-7
references: 24709358
references: Proc Natl Acad Sci U S A. 1981 Aug;78(8):5221-4
references: 6946469
references: PLoS One. 2014;9(9):e107767
references: 25225900
references: Pediatr Endocrinol Rev. 2011 Dec;9(2):549-53
references: 22397139
references: Arch Oral Biol. 2012 Nov;57(11):1474-81
references: 22858065
references: Mol Neurodegener. 2014;9:4
references: 24405708
references: Mol Cell. 2000 Jul;6(1):117-26
references: 10949033
references: Bioinformatics. 2008 Jul 1;24(13):i232-40
references: 18586719
references: Biomed Res Int. 2013;2013:267375
references: 23762832
references: J Neurosci. 2014 Feb 19;34(8):2921-30
references: 24553933
references: Mol Syst Biol. 2007;3:88
references: 17353930
references: Neuroscience. 2008 Jul 17;154(4):1417-22
references: 18534766
references: Cancer Cell. 2007 Aug;12(2):108-13
references: 17692803
references: Curr Opin Neurobiol. 2000 Jun;10(3):392-9
references: 10851180
references: Proc Natl Acad Sci U S A. 2006 Jul 11;103(28):10747-52
references: 16815967
references: Nat Rev Drug Discov. 2004 Aug;3(8):673-83
references: 15286734
references: J Immunol. 2000 Apr 15;164(8):4071-9
references: 10754300
references: BMC Syst Biol. 2008;2:67
references: 18652654
references: Apoptosis. 2009 Apr;14(4):584-96
references: 19156528
references: Science. 1999 Apr 16;284(5413):479-82
references: 10205054
references: Nephrol Dial Transplant. 2002;17 Suppl 9:8-10
references: 12386274
references: Gene. 2010 Jan 15;450(1-2):103-8
references: 19909801
references: Mol Cell. 2008 Aug 8;31(3):347-59
references: 18691967
references: J Neurosci Res. 2010 Sep;88(12):2641-7
references: 20648653
references: Cell. 1990 Sep 21;62(6):1073-85
references: 2205396
references: Cell. 2003 Oct 17;115(2):163-75
references: 14567914
references: In Silico Biol. 2005;5(2):111-28
references: 15972016
references: Eur J Neurosci. 2004 Dec;20(12):3259-69
references: 15610158
references: J Biol Chem. 2009 Jan 30;284(5):3158-69
references: 19059911
references: PLoS One. 2011;6(1):e14556
references: 21283518
references: Dev Biol. 2012 Apr 15;364(2):114-27
references: 22326227
references: Microsc Res Tech. 2011 Feb;74(2):153-8
references: 21275003
references: Nat Protoc. 2009;4(1):44-57
references: 19131956
references: J Neurosci. 2009 Aug 5;29(31):9714-8
references: 19657024
references: PLoS One. 2011;6(7):e22187
references: 21765950
references: J Pathol. 2014 Mar;232(4):415-27
references: 24293274
references: Nat Genet. 2000 May;25(1):25-9
references: 10802651
references: Hum Mol Genet. 1998 May;7(5):813-22
references: 9536085
references: Nature. 1996 Jul 18;382(6588):225-30
references: 8717036
references: J Neurosci Res. 2006 Apr;83(5):845-56
references: 16477652
references: Dev Growth Differ. 2011 Feb;53(2):137-48
references: 21338340
references: Protein Pept Lett. 2012 Sep;19(9):910-6
references: 22486617