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Article Open Access

Identification of altered pathways in breast cancer based on individualized pathway aberrance score

  • Authors:
    • Sheng‑Hong Shi
    • Wei Zhang
    • Jing Jiang
    • Long Sun
  • View Affiliations / Copyright

    Affiliations: Department of Breast Surgery, Ningbo No. 2 Hospital, Ningbo, Zhejiang 315000, P.R. China
    Copyright: © Shi et al. This is an open access article distributed under the terms of Creative Commons Attribution License.
  • Pages: 1287-1294
    |
    Published online on: June 1, 2017
       https://doi.org/10.3892/ol.2017.6292
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Abstract

The objective of the present study was to identify altered pathways in breast cancer based on the individualized pathway aberrance score (iPAS) method combined with the normal reference (nRef). There were 4 steps to identify altered pathways using the iPAS method: Data preprocessing conducted by the robust multi‑array average (RMA) algorithm; gene‑level statistics based on average Z; pathway‑level statistics according to iPAS; and a significance test dependent on 1 sample Wilcoxon test. The altered pathways were validated by calculating the changed percentage of each pathway in tumor samples and comparing them with pathways from differentially expressed genes (DEGs). A total of 688 altered pathways with P<0.01 were identified, including kinesin (KIF)‑ and polo‑like kinase (PLK)‑mediated events. When the percentage of change reached 50%, 310 pathways were involved in the total 688 altered pathways, which may validate the present results. In addition, there were 324 DEGs and 155 common genes between DEGs and pathway genes. DEGs and common genes were enriched in the same 9 significant terms, which also were members of altered pathways. The iPAS method was suitable for identifying altered pathways in breast cancer. Altered pathways (such as KIF and PLK mediated events) were important for understanding breast cancer mechanisms and for the future application of customized therapeutic decisions.
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Copy and paste a formatted citation
Spandidos Publications style
Shi SH, Zhang W, Jiang J and Sun L: Identification of altered pathways in breast cancer based on individualized pathway aberrance score. Oncol Lett 14: 1287-1294, 2017.
APA
Shi, S., Zhang, W., Jiang, J., & Sun, L. (2017). Identification of altered pathways in breast cancer based on individualized pathway aberrance score. Oncology Letters, 14, 1287-1294. https://doi.org/10.3892/ol.2017.6292
MLA
Shi, S., Zhang, W., Jiang, J., Sun, L."Identification of altered pathways in breast cancer based on individualized pathway aberrance score". Oncology Letters 14.2 (2017): 1287-1294.
Chicago
Shi, S., Zhang, W., Jiang, J., Sun, L."Identification of altered pathways in breast cancer based on individualized pathway aberrance score". Oncology Letters 14, no. 2 (2017): 1287-1294. https://doi.org/10.3892/ol.2017.6292
Copy and paste a formatted citation
x
Spandidos Publications style
Shi SH, Zhang W, Jiang J and Sun L: Identification of altered pathways in breast cancer based on individualized pathway aberrance score. Oncol Lett 14: 1287-1294, 2017.
APA
Shi, S., Zhang, W., Jiang, J., & Sun, L. (2017). Identification of altered pathways in breast cancer based on individualized pathway aberrance score. Oncology Letters, 14, 1287-1294. https://doi.org/10.3892/ol.2017.6292
MLA
Shi, S., Zhang, W., Jiang, J., Sun, L."Identification of altered pathways in breast cancer based on individualized pathway aberrance score". Oncology Letters 14.2 (2017): 1287-1294.
Chicago
Shi, S., Zhang, W., Jiang, J., Sun, L."Identification of altered pathways in breast cancer based on individualized pathway aberrance score". Oncology Letters 14, no. 2 (2017): 1287-1294. https://doi.org/10.3892/ol.2017.6292
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