Skip to main content

Selection of the Most Informative Genes in the Task of Cancer Tumors Recognition Based on the Gene Expression Profile

  • Conference paper
  • First Online:
Software Engineering Perspectives in Intelligent Systems (CoMeSySo 2020)

Part of the book series: Advances in Intelligent Systems and Computing ((AISC,volume 1295))

Included in the following conference series:

  • 624 Accesses

Abstract

The work considers the problem of selecting the most informative genes in the task of cancer tumors recognition based on the gene expression profile. The model of a cancer classifier based on a feedforward neural network is proposed. The most informative genes were selected using the layer-wise relevance propagation (LRP) method. The statistical methods were used to check the selected genes for relations to cancer.

This is a preview of subscription content, log in via an institution to check access.

Access this chapter

Subscribe and save

Springer+ Basic
$34.99 /Month
  • Get 10 units per month
  • Download Article/Chapter or eBook
  • 1 Unit = 1 Article or 1 Chapter
  • Cancel anytime
Subscribe now

Buy Now

Chapter
USD 29.95
Price excludes VAT (USA)
  • Available as PDF
  • Read on any device
  • Instant download
  • Own it forever
eBook
USD 129.00
Price excludes VAT (USA)
  • Available as EPUB and PDF
  • Read on any device
  • Instant download
  • Own it forever
Softcover Book
USD 169.99
Price excludes VAT (USA)
  • Compact, lightweight edition
  • Dispatched in 3 to 5 business days
  • Free shipping worldwide - see info

Tax calculation will be finalised at checkout

Purchases are for personal use only

Institutional subscriptions

Similar content being viewed by others

References

  1. Bach, S., Binder, A., Montavon, G., Klauschen, F., Müller, K.-R., Samek, W.: On pixel-wise explanations for non-linear classifier decisions by layer-wise relevance propagation. PLoS One 10(7) (2015). https://doi.org/10.1371/journal.pone.0130140

  2. Böhle, M., Eitel, F., Weygandt, M., Ritter, K.: Layer-wise relevance propagation for explaining deep neural network decisions in MRI-based Alzheimer’s disease classification. Front. Aging Neurosci. 10, (2019). https://doi.org/10.3389/fnagi.2019.00194

  3. Brägelmann, J., Klümper, N., Offermann, A., von Mässenhausen, A., Böhm, D., Deng, M., Queisser, A., Sanders, C., Syring, I., Merseburger, A.S., Vogel, W., Sievers, E., Vlasic, I., Carlsson, J., Andrén, O., Brossart, P., Duensing, S., Svensson, M.A., Shaikhibrahim, Z., Kirfel, J., Perner, S.: Pan-Cancer analysis of the mediator complex transcriptome identifies CDK19 and CDK8 as therapeutic targets in advanced prostate cancer. Clin. Cancer Res. 23, 1829–1840 (2017). https://doi.org/10.1158/1078-0432.CCR-16-0094

    Article  Google Scholar 

  4. Chen, J., Bardes, E.E., Aronow, B.J., Jegga, A.G.: ToppGene suite for gene list enrichment analysis and candidate gene prioritization. Nucleic Acids Res. 37, 305–311 (2009). https://doi.org/10.1093/nar/gkp427

    Article  Google Scholar 

  5. Danaee, P., Ghaeini, R., Hendrix, D.A.: A deep learning approach for cancer detection and relevant gene identification. Pac. Symp. Biocomput. 22, 219–229 (2016). https://doi.org/10.1142/9789813207813_0022

    Article  Google Scholar 

  6. De Guia, J.M., Devaraj, M., Leung, C.K.: DeepGX: deep learning using gene expression for cancer classification. In: Proceedings of the 2019 IEEE/ACM International Conference on Advances in Social Networks Analysis and Mining, ASONAM 2019, pp. 913–920. Association for Computing Machinery, Inc., New York (2019)

    Google Scholar 

  7. Li, Y., Kang, K., Krahn, J.M., Croutwater, N., Lee, K., Umbach, D.M., Li, L.: A comprehensive genomic pan-cancer classification using the cancer genome atlas gene expression data. BMC Genom. 18, 508 (2017). https://doi.org/10.1186/s12864-017-3906-0

    Article  Google Scholar 

  8. Lyu, B., Haque, A.: Deep learning based tumor type classification using gene expression data. In: Proceedings of the 2018 ACM International Conference on Bioinformatics, Computational Biology, and Health Informatics, Washington, DC, USA, pp. 89–96 (2018). https://doi.org/10.1101/364323

  9. Muzny, D., Bainbridge, M., Chang, K., et al.: Comprehensive molecular characterization of human colon and rectal cancer. Nature 487, 330–337 (2012). https://doi.org/10.1038/nature11252

    Article  Google Scholar 

  10. Pavlov, K.A., Korchagina, A.A., Abdulina, Y.A., Surenkov, D.N., Zus’man, L.A., Darenkov, S.P., Grigor’ev, M.E., CHekhonin, V.P.: PCA3—perspektivnyj biomarker raka predstatel’noj zhelezy (PCA3 — Promising Prostate Cancer Biomarker). Vestnik Rossijskogo gosudarstvennogo medicinskogo universiteta 3, 54–58 (2012)

    Google Scholar 

  11. Perevodchikova, N.I., Stenina, M.B.: Lekarstvennaya terapiya raka molochnoj zhelezy (Breast Cancer Drug Treatment). Praktika, Moscow (2014)

    Google Scholar 

  12. Shitikov, V.K., Rozenberg, G.S.: Randomizaciya i butstrep: statisticheskij analiz v biologii i ekologii s ispol’zovaniem R (Randomization and bootstrap: statistical analysis in biology and ecology using R). Kassandra, Tolyatti (2013)

    Google Scholar 

  13. UCSC Xena. The Cancer Genome Atlas (2020). https://tcga.xenahubs.net. Accessed 10 May 2020

  14. Yu, H., Samuels, D.C., Zhao, Y., Guo, Y.: Architectures and accuracy of artificial neural network for disease classification from omics data. BMC Genom. 20, 167 (2019). https://doi.org/10.1186/s12864-019-5546-z

    Article  Google Scholar 

Download references

Author information

Authors and Affiliations

Authors

Corresponding author

Correspondence to Alexey Kruzhalov .

Editor information

Editors and Affiliations

Appendix

Appendix

(See Table 3).

Table 3. Recognition accuracy estimation

Rights and permissions

Reprints and permissions

Copyright information

© 2020 The Editor(s) (if applicable) and The Author(s), under exclusive license to Springer Nature Switzerland AG

About this paper

Check for updates. Verify currency and authenticity via CrossMark

Cite this paper

Kruzhalov, A., Philippovich, A. (2020). Selection of the Most Informative Genes in the Task of Cancer Tumors Recognition Based on the Gene Expression Profile. In: Silhavy, R., Silhavy, P., Prokopova, Z. (eds) Software Engineering Perspectives in Intelligent Systems. CoMeSySo 2020. Advances in Intelligent Systems and Computing, vol 1295. Springer, Cham. https://doi.org/10.1007/978-3-030-63319-6_83

Download citation

Publish with us

Policies and ethics