Abstract
Correlation analysis, first invented by Francis Galton and later scientifically conceptualised by Karl Pearson, has many powerful applications in biology for describing causality in biological systems. Ever since the 1920s, causation has been connected with correlation in this way. The underlying mechanisms in biological processes are shadowed in correlations that when analysed can reveal connections in biological data that provide a starting point to realise underlying biological processes.
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
Agren R, Bordel S, Mardinoglu A, Pornputtapong N, Nookaew I, Nielsen J (2012) Reconstruction of genome-scale active metabolic networks for 69 human cell types and 16 cancer types using INIT. PLoS Comput Biol 8(5):e1002518. doi:10.1371/journal.pcbi.1002518
Camacho D, de la FA, Mendes P (2005) The origin of correlations in metabolomics data. Metabolomics 1(1):53–63. doi:10.1007/s11306-005-1107-3
Duarte NC, Becker SA, Jamshidi N, Thiele I, Mo ML, Vo TD, Srivas R, Palsson BO (2007) Global reconstruction of the human metabolic network based on genomic and bibliomic data. Proc Natl Acad Sci U S A 104(6):1777–1782. doi:10.1073/pnas0610772104
Fisher RA (1915) Frequency distribution of the values of the correlation coefficient in samples from an indefinitely large population. Biometrika 10(4):507–521
Kanehisa M, Goto S (2000) KEGG: Kyoto Encyclopedia of genes and genomes. Nucleic Acids Res 28(1):27–30. doi:10.1093/nar/28.1.27
Kotze H, Armitage E, Sharkey K, Allwood J, Dunn W, Williams K, Goodacre R (2013) A novel untargeted metabolomics correlation-based network analysis incorporating human metabolic reconstructions. BMC Syst Biol 7(1):107
Ma H, Zeng A-P (2003) Reconstruction of metabolic networks from genome data and analysis of their global structure for various organisms. Bioinformatics 19(2):270–277
Ma HW, Sorokin A, Mazein A, Selkov A, Selkov E, Demin O, Goryanin I (2007) The Edinburgh human metabolic network reconstruction and its functional analysis. Mol Syst Biol 3:135. doi:10.1038/msb4100177
Mardinoglu A, Agren R, Kampf C, Asplund A, Nookaew I, Jacobson P, Walley AJ, Froguel P, Carlsson LM, Uhlen M, Nielsen J (2013) Integration of clinical data with a genome-scale metabolic model of the human adipocyte. Mol Syst Biol 9:649. doi:10.1038/msb.2013.5
Rodgers JL, Nicewander WA (1988) Thirteen ways to look at the correlation coefficient. Am Stat 42(1):59–66
Shipley B (2004) Cause and correlation in biology: a user’s guide to path analysis, structural equations and causal inference, 1st edn. Cambridge University Press, Cambridge
Steuer R (2006) Review: on the analysis and interpretation of correlations in metabolomic data. Brief Bioinform 7(2):151–158
Stifanelli P, Creanza T, Anglani R, Liuzzi V, Mukherjee S, Ancona N (2011) A comparative study of Gaussian Graphical Model approaches for genomic data. arXiv preprint arXiv:11070261
Thiele I, Swainston N, Fleming RMT, Hoppe A, Sahoo S, Aurich MK, Haraldsdottir H, Mo ML, Rolfsson O, Stobbe MD, Thorleifsson SG, Agren R, Boelling C, Bordel S, Chavali AK, Dobson P, Dunn WB, Endler L, Hala D, Hucka M, Hull D, Jameson D, Jamshidi N, Jonsson JJ, Juty N, Keating S, Nookaew I, Le Novere N, Malys N, Mazein A, Papin JA, Price ND, Selkov E Sr, Sigurdsson MI, Simeonidis E, Sonnenschein N, Smallbone K, Sorokin A, van Beek JHGM, Weichart D, Goryanin I, Nielsen J, Westerhoff HV, Kell DB, Mendes P, Palsson BO (2013) A community-driven global reconstruction of human metabolism. Nat Biotechnol 31(5):419–425. doi:10.1038/nbt.2488
Toni T, Tidor B (2013) Combined model of intrinsic and extrinsic variability for computational network design with application to synthetic biology. PLoS Comput Biol 9(3):e1002960
Wishart DS, Knox C, Guo AC, Eisner R, Young N, Gautam B, Hau DD, Psychogios N, Dong E, Bouatra S, Mandal R, Sinelnikov I, Xia J, Jia L, Cruz JA, Lim E, Sobsey CA, Shrivastava S, Huang P, Liu P, Fang L, Peng J, Fradette R, Cheng D, Tzur D, Clements M, Lewis A, De Souza A, Zuniga A, Dawe M, Xiong Y, Clive D, Greiner R, Nazyrova A, Shaykhutdinov R, Li L, Vogel HJ, Forsythe I (2009) HMDB: a knowledgebase for the human metabolome. Nucleic Acids Res 37:D603–D610. doi:10.1093/nar/gkn810
Author information
Authors and Affiliations
Corresponding author
Rights and permissions
Copyright information
© 2014 The Authors
About this chapter
Cite this chapter
Armitage, E., Kotze, H., Williams, K. (2014). Network-Based Correlation Analysis of Metabolic Fingerprinting Data. In: Correlation-based network analysis of cancer metabolism. SpringerBriefs in Systems Biology. Springer, New York, NY. https://doi.org/10.1007/978-1-4939-0615-4_4
Download citation
DOI: https://doi.org/10.1007/978-1-4939-0615-4_4
Published:
Publisher Name: Springer, New York, NY
Print ISBN: 978-1-4939-0614-7
Online ISBN: 978-1-4939-0615-4
eBook Packages: Biomedical and Life SciencesBiomedical and Life Sciences (R0)