Open Access Research article

Identification of genes with a correlation between copy number and expression in gastric cancer

Lei Cheng14, Ping Wang2, Sheng Yang1, Yanqing Yang1, Qing Zhang3, Wen Zhang4, Huasheng Xiao4, Hengjun Gao4* and Qinghua Zhang14*

Author Affiliations

1 State Key Laboratory of Medical Genomics and Shanghai Institute of Hematology, Ruijin Hospital, Shanghai Jiaotong University School of Medicine, Shanghai, China

2 Department of Pathology, Ninth People's Hospital, Shanghai Jiaotong University School of Medicine, Shanghai, China

3 Department of Oncology, Gongli Hospital, Shanghai, China

4 National Engineering Center for Biochip at Shanghai, Shanghai, China

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BMC Medical Genomics 2012, 5:14  doi:10.1186/1755-8794-5-14

Published: 4 May 2012

Additional files

Additional file 1:

Table S3. The 27 pairs of gastric samples were analyzed by aCGH using Agilent CGH Analytics 4.0.76 software. ADM-2 algorithm with a threshold level of 4 was used to identify CNVs in individual samples. CNVs, copy number variations.

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Additional file 2:

Table S4. Copy number associated gene expression changes. Pearson correlation coefficients between DNA copy number aberrations and alterations in mRNA expression level for each selected gene were calculated in SPSS 11.5 software. Gene expression referred to log2 ratios from gene expression profiling. Normal and Tumor referred to an average log2 ratio of 25 pairs of gastric samples, respectively. aCGH log2 ratio referred to an average log2 ratio for only those cases (Frequency) in which the ratio was over 1.5-fold changed (log2 ratio ≥ 0.585 or ≤ −0.585). firstly, a mean log2 copy number variation ratio was calculated for all the probes targeting the same gene. Then, the Pearson’s r was measured between aCGH and gene expression profiling performed in 25 pairs of gastric samples.

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Additional file 3:

Figure S2. An unsupervised hierarchical clustering of 50 gastric samples with 163 genes revealed two distinct clusters. Log ratio scale bar for the Treeview color change was also shown. Suffix “T” indicates gastric cancer samples; “N” indicates matched adjacent noncancerous samples.

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Additional file 4:

Figure S3. Correlation between copy number ratios and expression ratios in representative genes (XPO5 and MCM4). The X axis showed 25 gastric samples and the Y axis displayed log ratios of copy number and gene expression from microarrays.

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Additional file 5:

Table S1. Clinical and histological data of the 27 pairs of gastric samples. M, male; F, female; ADC, adenocarcinoma; SRCC, signet-ring cell carcinoma; T, invasion activity; N, lymph node colonization; M, metastasis; Dif, differentiation; Hp, helicobacter pylori; MD, moderately differentiated; PD, poorly differentiated; M-PD, moderately-poorly differentiated; NA, not available.

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Additional file 6:

Figure S1. Efficiency of cell capturing. Noncancerous mucosa (A) before and (B) after dissection of the epithelia. (C) Image of the epithelium on the cap. Tumor cells in muscle layer (D) before and (E) after dissection of the tumor cells. (F) Image of the tumor cell on the cap.

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Additional file 7:

Table S2. All primers were used in the qRT-PCR validation of gene expression microarray data.

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