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Open Access Highly Accessed Open Badges Research article

Genome-wide analysis of three-way interplay among gene expression, cancer cell invasion and anti-cancer compound sensitivity

Yi-Chiung Hsu12, Hsuan-Yu Chen1, Shinsheng Yuan1, Sung-Liang Yu3, Chia-Hung Lin1, Guani Wu1, Pan-Chyr Yang245 and Ker-Chau Li16*

Author Affiliations

1 Institute of Statistical Science, Academia Sinica, 128 Academia Road, Section 2, Taipei, 115, Taiwan

2 NTU Research Center for Medical Excellence - Division of Genomic Medicine, 2 Syu-Jhou Road, Taipei, 100, Taiwan

3 Department of Clinical Laboratory Sciences and Medical Biotechnology, National Taiwan University College of Medicine, 1 Chang-Te Street, Taipei, 100, Taiwan

4 Department of Internal Medicine, National Taiwan University College of Medicine, 1 Jen-Ai Road, Taipei, 100, Taiwan

5 Institute of Biomedical Sciences Academia Sinica, 128 Academia Road, Section 2, Taipei, 115, Taiwan

6 Department of Statistics, University of California, Los Angeles, Los Angeles, CA, 90095, USA

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BMC Medicine 2013, 11:106  doi:10.1186/1741-7015-11-106

Published: 16 April 2013

Additional files

Additional file 1:

Supplementary information. Procedures for determining the invasion-associated (IA) genes. II. Combination use of anti-microtubule and targeted therapy agents. Figure S1. Histogram of invaded cell counts (ICC) after subtracting the tissue-group means. Figure S2. Cell adhesion: Integrin-mediated cell adhesion and migration pathway. Figure S3. The heatmap for the correlations between 744 IA gene expression and 99 drug response (−logGI50) in NCI-60 cell lines. Figure S4. Validation of microarray gene expression data with qPCR. Figure S5. Plots of the eight-gene risk scores between drug sensitive and drug resistant groups of cell lines after removing the nine cell lines that came from the NCI60 panel. The dotted line indicated the mean of each group. Figure S6. Kaplan–Meier survival curves for survival analysis of the eight-gene signature in breast and lung cancer patients who did not receive systemic treatment. Figure S7. Kaplan–Meier survival curves for survival analysis of the four-gene signature in lung cancer and breast cancer cohorts. Table S1. The expression level of eight signature genes in the nine NCI-60 cell lines. Table S2. TaqMan probes ID for eight gene expression validation. Table S3. Enrichment analysis of 633 invasion-associated genes by functional ontology enrichment tool in MetaCore. Table S4. The correlation matrix for (A) anti-microtubule and for (B) targeted therapy drugs. Table S5. Genes having significant gene-drug correlation with everolimus, dasatinib, erlotinib, paclitaxel and docetaxel profiles. The final list of eight IA-genes is shown in bold face. Table S6. Correlation between the invasion profile and each of the 99 drug sensitivity profiles of NCI60 cell lines. The significant correlation (P <0.05) is shown in bold face.

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