Open Access Research article

Systematically characterizing and prioritizing chemosensitivity related gene based on Gene Ontology and protein interaction network

Xin Chen, Wei Jiang, Qianghu Wang, Teng Huang, Peng Wang, Yan Li, Xiaowen Chen, Yingli Lv and Xia Li*

Author Affiliations

College of Bioinformatics Science and Technology, Harbin Medical University, Harbin, 150081, China

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BMC Medical Genomics 2012, 5:43  doi:10.1186/1755-8794-5-43

Published: 2 October 2012

Additional files

Additional file 1:

Table S4. Detailed description of drug-CCRG pairs.

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Additional file 2:

Figure S1. The comparison of drug-CCRG PCC with random PCC for each of the 62 drug-CCRG pairs. Each subfigure of this figure shows the location of Pearson's correlation coefficient (PCC) of a drug-CCRG pair in all the drug-gene pairs. The red line represents the PCC of a drug-CCRG pair, while the blue curves shows the distribution of PCC of all the drug-gene pairs. The x-axis shows the PCC of drug-gene pair. The y-axis shows the probability density value of PCC.

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Additional file 3:

Table S1. A full list of CCRG enriched GO terms.

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Additional file 4:

Table S2. CCRG enriched GO terms have higher similarity than that of random genes.

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Additional file 5:

Figure S2. Detailed performance comparison under all the 20 thresholds. Figure A to Figure T shows the comparison result of two methods to identify CCRGs under 20 sets of thresholds. A is the result under the following threshold: degree_threshold: percentile 1 (0.01), betweenness centrality_threshold: percentile 1(0.01). B is the result under the threshold: degree_threshold: percentile 2 (0.02), betweenness centrality_threshold: percentile 2 (0.02). And the corollary, Figure T is the result under the threshold: degree_threshold: percentile 20 (0.20), betweenness centrality_threshold: percentile 20 (0.20). The text over each figure is the area under curve (AUC). Take Figure A for example, 0.7087 vs 0.5446 represents that AUC of our method is 0.7087, and 0.5446 is AUC of traditional method based on gene expression. The AUC is colored according to curve color.

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Additional file 6:

Table S3. The full list of predicted chemosensitivity related genes.

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