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RETRACTED ARTICLE: Text mining and network analysis of molecular interaction in non-small cell lung cancer by using natural language processing

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This article was retracted on 18 August 2015

Abstract

Lung cancer including non-small cell lung cancer (NSCLC) and small cell lung cancer is one of the most aggressive tumors with high incidence and low survival rate. The typical NSCLC patients account for 80–85 % of the total lung cancer patients. To systemically explore the molecular mechanisms of NSCLC, we performed a molecular network analysis between human and mouse to identify key genes (pathways) involved in the occurrence of NSCLC. We automatically extracted the human-to-mouse orthologous interactions using the GeneWays system by natural language processing and further constructed molecular (gene and its products) networks by mapping the human-to-mouse interactions to NSCLC-related mammalian phenotypes, followed by module analysis using ClusterONE of Cytoscape and pathway enrichment analysis using the database for annotation, visualization and integrated discovery (DAVID) successively. A total of 70 genes were proven to be related to the mammalian phenotypes of NSCLC, and seven genes (ATAD5, BECN1, CDKN2A, FNTB, E2F1, KRAS and PTEN) were found to have a bearing on more than one mammalian phenotype (MP) each. Four network clusters centered by four genes thyroglobulin (TG), neurofibromatosis type-1 (NF1 ), neurofibromatosis type 2 (NF2 ) and E2F transcription factor 1 (E2F1) were generated. Genes in the four network modules were enriched in eight KEGG pathways (p value < 0.05), including pathways in cancer, small cell lung cancer, cell cycle and p53 signaling pathway. Genes p53 and E2F1 may play important roles in NSCLC occurrence, and thus can be considered as therapeutic targets for NSCLC.

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Acknowledgments

We wish to express our warm thanks to Fenghe (Shanghai) Information Technology Co., Ltd. Their ideas and help gave a valuable added dimension to our research.

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Authors and Affiliations

  1. Department of Hematology and Oncology, China-Japan Union Hospital of Jilin University, Changchun, 130031, Jilin, People’s Republic of China

    Jun Li, Lintao Bi, Yanxia Sun, Zhenxia Lu, Yumei Lin & Hui Shao

  2. Tumor Center, Jilin University First Hospital, No. 261 Xinminda Street, Changchun, 130021, Jilin, People’s Republic of China

    Ou Bai

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  1. Jun Li
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  2. Lintao Bi
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  3. Yanxia Sun
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  4. Zhenxia Lu
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  7. Hui Shao
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Correspondence to Ou Bai.

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The Publisher and Editor retract this article in accordance with the recommendations of the Committee on Publication Ethics (COPE). After a thorough investigation we have strong reason to believe that the peer review process was compromised.

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Li, J., Bi, L., Sun, Y. et al. RETRACTED ARTICLE: Text mining and network analysis of molecular interaction in non-small cell lung cancer by using natural language processing. Mol Biol Rep 41, 8071–8079 (2014). https://doi.org/10.1007/s11033-014-3705-5

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