Abstract
The comparison of biological networks is a crucial step to better understanding the underlying mechanisms involved in specific experimental conditions, such as those of health and disease or high and low concentrations of an environmental element. To this end, several tools have been developed to compare whether network structures are “equal” (in some sense) across conditions. Some examples of computational methods include DCGL, EBcoexpress, DiffCorr, CoDiNA, DiffCoEx, coXpress, DINGO, DECODE, dCoxS, GSCA, GSNCA, CoGA, GANOVA, and BioNetStat. We will briefly describe these algorithms and their advantages and disadvantages.
This is a preview of subscription content, log in via an institution to check access.
Access this chapter
Tax calculation will be finalised at checkout
Purchases are for personal use only
References
Santos SDS, Takahashi DY, Nakata A, Fujita A (2013) Brief Bioinform 15(6):906. https://doi.org/10.1093/bib/bbt051
Langfelder P, Horvath S (2008) BMC Bioinform 9:559. https://doi.org/10.1186/1471-2105-9-559
Caldana C, Degenkolbe T, Cuadros-Inostroza A, Klie S, Sulpice R, Leisse A, Steinhauser D, Fernie AR, Willmitzer L, Hannah MA (2011) Plant J 67(5):869. https://doi.org/10.1111/j.1365-313X.2011.04640.x
Weston DJ, Karve AA, Gunter LE, Jawdy SS, Yang X, Allen SM, Wullschleger SD (2011) Plant, Cell Environ 34(9):1488. https://doi.org/10.1111/j.1365-3040.2011.02347.x
Zhang H, Yin T (2016) Tree Genet Genomes 12(3):61. https://doi.org/10.1007/s11295-016-1016-9
Sun SY, Liu ZP, Zeng T, Wang Y, Chen L (2013) Scientific reports 3:2268. https://doi.org/10.1038/srep02268, http://www.pubmedcentral.nih.gov/articlerender.fcgi?artid=3721080&tool=pmcentrez&rendertype=abstract
Walley AJ, Jacobson P, Falchi M, Bottolo L, Andersson JC, Petretto E (2012) Int J 36(1):137. https://doi.org/10.1038/ijo.2011.22.Differential
Hochberg U, Degu A, Toubiana D, Gendler T, Nikoloski Z, Rachmilevitch S, Fait A (2013) BMC Plant Biol 13(1):184. https://doi.org/10.1186/1471-2229-13-184, http://dx.plos.org/10.1371/journal.pone.0115581://www.biomedcentral.com/1471-2229/13/184
Fukushima A (2013) Gene 518(1):209. https://doi.org/10.1016/j.gene.2012.11.028
Fisher RA (1915) Biometrika 10(4):507. www.jstor.org/stable/2331838
Liu BH, Yu H, Tu K, Li C, Li YX, Li YY (2010) Bioinformatics 26(20):2637. https://doi.org/10.1093/bioinformatics/btq471
Yu H, Liu BH, Ye ZQ, Li C, Li YX, Li YY (2011) BMC Bioinform 12(1):315. https://doi.org/10.1186/1471-2105-12-315, http://www.pubmedcentral.nih.gov/articlerender.fcgi?artid=3199761&tool=pmcentrez&rendertype=abstract
Dawson JA, Ye S, Kendziorski C (2012) Bioinformatics 28(14):1939. https://doi.org/10.1093/bioinformatics/bts268
Siska C, Bowler R, Kechris K (2015) Bioinformatics 32(5):690. https://doi.org/10.1093/bioinformatics/btv633
Singh AJ, Ramsey SA, Filtz TM, Kioussi C (2018) Cell Mol Life Sci 75(6):1013. https://doi.org/10.1007/s00018-017-2679-6
McKenzie AT, Katsyv I, Song WM, Wang M, Zhang B (2016) BMC Syst Biol 10(1):106. https://doi.org/10.1186/s12918-016-0349-1, http://www.ncbi.nlm.nih.gov/pubmed/27846853%5Cnwww.pubmedcentral.nih.gov/articlerender.fcgi?artid=PMC5111277
Ha MJ, Baladandayuthapani V, Do KA (2015) Bioinformatics 31(21):3413. https://doi.org/10.1093/bioinformatics/btv406
Tesson BM, Breitling R, Jansen RC (2010) BMC Bioinform 11(1):497. https://doi.org/10.1186/1471-2105-11-497, http://bmcbioinformatics.biomedcentral.com/articles/
Watson M (2006) BMC Bioinform 7:509. https://doi.org/10.1186/1471-2105-7-509, http://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pubmed&id=17116249&retmode=ref&cmd=prlinks%5Cnpapers3://publication/
Amar D, Safer H, Shamir R (2013) PLoS Comput Biol 9:3. https://doi.org/10.1371/journal.pcbi.1002955
Bockmayr M, Klauschen F, Györffy B, Denkert C, Budczies J (2013) BMC Syst Biol 7(1):78. https://doi.org/10.1186/1752-0509-7-78, http://www.ncbi.nlm.nih.gov/pubmed/23945349%5Cnwww.biomedcentral.com/1752-0509/7/78
Wang D, Gu J (2016) Quant Biol 4(1):58. https://doi.org/10.1007/s40484-016-0063-4
Kayano M, Takigawa I, Shiga M, Tsuda K, Mamitsuka H (2011) Nucl Acids Res 39(11):1. https://doi.org/10.1093/nar/gkr130
Lui TWH, Tsui NBY, Chan LWC, Wong CSC, Siu PMF, Yung BYM (2015) BMC Bioinform 16(1):182. https://doi.org/10.1186/s12859-015-0582-4, http://bmcbioinformatics.biomedcentral.com/articles/
Cho SB, Kim J, Kim JH (2009) BMC Bioinform 10(1):109. https://doi.org/10.1186/1471-2105-10-109
Choi Y, Kendziorski C (2009) Bioinformatics. https://doi.org/10.1093/bioinformatics/btp502
Rahmatallah Y, Emmert-Streib F, Glazko G (2014) Bioinformatics 30(3):360. https://doi.org/10.1093/bioinformatics/btt687
Bonacich P (1972) Sociol Methodol 4:176. https://www.jstor.org/stable/270732
Santos SDS, De Almeida Galatro TF, Watanabe RA, Oba-Shinjo SM, Marie SKN, Fujita A (2015) PLoS ONE. https://doi.org/10.1371/journal.pone.0135831
Fujita A, Vidal MC, Takahashi DY (2017) Front Neurosci 11. https://doi.org/10.3389/fnins.2017.00066, http://journal.frontiersin.org/article/10.3389/fnins.2017.00066/full
Jardim VC, Santos SSS, Fujita A, Buckeridge MS (2019) Front Genet 10(1). https://doi.org/10.3389/fgene.2019.00594
Acknowledgements
This work was partially supported by FAPESP (2018/21934-5, 2019/03615-2), CAPES (Finance Code 001), CNPq (303855/2019-3), Alexander von Humboldt Foundation, Newton Fund, and The Academy of Medical Sciences.
Author information
Authors and Affiliations
Corresponding author
Editor information
Editors and Affiliations
Rights and permissions
Copyright information
© 2020 Springer Nature Switzerland AG
About this chapter
Cite this chapter
Jardim, V.C., Moreno, C.C., Fujita, A. (2020). Computational Tools for Comparing Gene Coexpression Networks. In: da Silva, F.A.B., Carels, N., Trindade dos Santos, M., Lopes, F.J.P. (eds) Networks in Systems Biology. Computational Biology, vol 32. Springer, Cham. https://doi.org/10.1007/978-3-030-51862-2_2
Download citation
DOI: https://doi.org/10.1007/978-3-030-51862-2_2
Published:
Publisher Name: Springer, Cham
Print ISBN: 978-3-030-51861-5
Online ISBN: 978-3-030-51862-2
eBook Packages: Computer ScienceComputer Science (R0)