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Chromosome-based gene co-expression analysis reveals regions associated with cancers: chromosome 1 as an example

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Gene co-expression network analysis has been widely performed in systems biology. Here, I use a chromosome-based strategy to find potential chromosome regions associated with disease, and show an example of cancer. All results are available at http://bioinformatics.fafu.edu.cn/chrom-WGCNA/.

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References

  1. Visscher PM, Brown MA, McCarthy MI, Yang J (2012) Five years of GWAS discovery. Am J Hum Genet 90(1):7–24. https://doi.org/10.1016/j.ajhg.2011.11.029

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  2. Freedman ML, Monteiro AN, Gayther SA, Coetzee GA, Risch A, Plass C, Casey G, De Biasi M, Carlson C, Duggan D, James M, Liu P, Tichelaar JW, Vikis HG, You M, Mills IG (2011) Principles for the post-GWAS functional characterization of cancer risk loci. Nat Genet 43(6):513–518. https://doi.org/10.1038/ng.840

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  3. Li H, Wang Y, Liu H, Shi Q, Xu Y, Wu W, Zhu D, Amos CI, Fang S, Lee JE, Han J, Wei Q (2017) Genetic variants in the integrin signaling pathway genes predict cutaneous melanoma survival. Int J Cancer 140(6):1270–1279. https://doi.org/10.1002/ijc.30545

    Article  CAS  PubMed  Google Scholar 

  4. Weng L, Macciardi F, Subramanian A, Guffanti G, Potkin SG, Yu Z, Xie X (2011) SNP-based pathway enrichment analysis for genome-wide association studies. BMC Bioinformatics 12:99. https://doi.org/10.1186/1471-2105-12-99

    Article  PubMed  PubMed Central  Google Scholar 

  5. Chen Y, Zhu J, Lum PY, Yang X, Pinto S, MacNeil DJ, Zhang C, Lamb J, Edwards S, Sieberts SK, Leonardson A, Castellini LW, Wang S, Champy MF, Zhang B, Emilsson V, Doss S, Ghazalpour A, Horvath S, Drake TA, Lusis AJ, Schadt EE (2008) Variations in DNA elucidate molecular networks that cause disease. Nature 452(7186):429–435. https://doi.org/10.1038/nature06757

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  6. Barabasi AL, Gulbahce N, Loscalzo J (2011) Network medicine: a network-based approach to human disease. Nat Rev Genet 12(1):56–68. https://doi.org/10.1038/nrg2918

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  7. Weiss JN, Karma A, MacLellan WR, Deng M, Rau CD, Rees CM, Wang J, Wisniewski N, Eskin E, Horvath S, Qu Z, Wang Y, Lusis AJ (2012) “Good enough solutions” and the genetics of complex diseases. Circ Res 111(4):493–504. https://doi.org/10.1161/CIRCRESAHA.112.269084

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  8. Langfelder P, Zhang B, Horvath S (2008) Defining clusters from a hierarchical cluster tree: the Dynamic Tree Cut package for R. Bioinformatics 24(5):719–720

    Article  CAS  PubMed  Google Scholar 

  9. De Preter K, Barriot R, Speleman F, Vandesompele J, Moreau Y (2008) Positional gene enrichment analysis of gene sets for high-resolution identification of overrepresented chromosomal regions. Nucleic Acids Res 36(7):e43. https://doi.org/10.1093/nar/gkn114

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  10. La Starza R, Crescenzi B, Pierini V, Romoli S, Gorello P, Brandimarte L, Matteucci C, Kropp MG, Barba G, Martelli MF, Mecucci C (2007) A common 93-kb duplicated DNA sequence at 1q21.2 in acute lymphoblastic leukemia and Burkitt lymphoma. Cancer Genet Cytogenet 175(1):73–76. https://doi.org/10.1016/j.cancergencyto.2007.01.011

    Article  CAS  PubMed  Google Scholar 

  11. Macgregor S, Montgomery GW, Liu JZ, Zhao ZZ, Henders AK, Stark M, Schmid H, Holland EA, Duffy DL, Zhang M, Painter JN, Nyholt DR, Maskiell JA, Jetann J, Ferguson M, Cust AE, Jenkins MA, Whiteman DC, Olsson H, Puig S, Bianchi-Scarra G, Hansson J, Demenais F, Landi MT, Debniak T, Mackie R, Azizi E, Bressac-de Paillerets B, Goldstein AM, Kanetsky PA, Gruis NA, Elder DE, Newton-Bishop JA, Bishop DT, Iles MM, Helsing P, Amos CI, Wei Q, Wang LE, Lee JE, Qureshi AA, Kefford RF, Giles GG, Armstrong BK, Aitken JF, Han J, Hopper JL, Trent JM, Brown KM, Martin NG, Mann GJ, Hayward NK (2011) Genome-wide association study identifies a new melanoma susceptibility locus at 1q21.3. Nat Genet 43(11):1114–1118. https://doi.org/10.1038/ng.958

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  12. Beroukhim R, Mermel CH, Porter D, Wei G, Raychaudhuri S, Donovan J, Barretina J, Boehm JS, Dobson J, Urashima M, Mc Henry KT, Pinchback RM, Ligon AH, Cho YJ, Haery L, Greulich H, Reich M, Winckler W, Lawrence MS, Weir BA, Tanaka KE, Chiang DY, Bass AJ, Loo A, Hoffman C, Prensner J, Liefeld T, Gao Q, Yecies D, Signoretti S, Maher E, Kaye FJ, Sasaki H, Tepper JE, Fletcher JA, Tabernero J, Baselga J, Tsao MS, Demichelis F, Rubin MA, Janne PA, Daly MJ, Nucera C, Levine RL, Ebert BL, Gabriel S, Rustgi AK, Antonescu CR, Ladanyi M, Letai A, Garraway LA, Loda M, Beer DG, True LD, Okamoto A, Pomeroy SL, Singer S, Golub TR, Lander ES, Getz G, Sellers WR, Meyerson M (2010) The landscape of somatic copy-number alteration across human cancers. Nature 463(7283):899–905. https://doi.org/10.1038/nature08822

    Article  CAS  PubMed  PubMed Central  Google Scholar 

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Acknowledgements

This work was supported in part by the National Natural Science Foundation of China (No. 81502091). I thank The Broad Institute of MIT & Harvard for sharing their Cancer Cell Line Encyclopedia project. I thank Catherine Perfect, MA (Cantab), from Liwen Bianji, Edanz Editing China (http://www.liwenbianji.cn/ac), for editing the English text of a draft of this manuscript.

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  1. School of Life Sciences, Fujian Agriculture and Forestry University, Fuzhou, 350002, China

    Wei Liu

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  1. Wei Liu
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Correspondence to Wei Liu.

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Liu, W. Chromosome-based gene co-expression analysis reveals regions associated with cancers: chromosome 1 as an example. Mol Biol Rep 46, 1551–1553 (2019). https://doi.org/10.1007/s11033-019-04596-y

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