Open Access Highly Accessed Research article

miRNA signature associated with outcome of gastric cancer patients following chemotherapy

Chang Hee Kim1, Hark K Kim23, R Luke Rettig1, Joseph Kim2, Eunbyul T Lee2, Olga Aprelikova2, Il J Choi3, David J Munroe1 and Jeffrey E Green2*

  • * Corresponding author: Jeffrey E Green jegreen@nih.gov

  • † Equal contributors

Author Affiliations

1 Advanced Technology Program, SAIC-Frederick, Inc., National Cancer Institute-Frederick, Frederick, MD 21701, USA

2 Laboratory of Cancer Biology and Genetics, National Cancer Institute, Bethesda, MD 20892, USA

3 National Cancer Center, Goyang, Gyeonggi, Republic of Korea, 410-769

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BMC Medical Genomics 2011, 4:79  doi:10.1186/1755-8794-4-79

Published: 23 November 2011

Additional files

Additional file 1:

Supplemental Figure 1: Validation of miR expression by quantitative real-time reverse transcription polymerase chain reaction (Q-RT-PCR). Q-RT-PCR analyses of miR-486 in 12 normal (circles) and 7 cancer samples (squares), confirming over-expression of miR-486 as observed in the microarray data of the cancer samples.

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Additional file 2:

Supplemental Table 1: Cross platform comparisons of miRNA expression. Comparing the data for detection of microRNAs in the same two tissue samples (brain and liver), the ABI Taqman Array MicroRNA Card platform and the Affymetrix/FlashTagHSR platforms demonstrated the highest percent present calls and were nearly identical on their respective platforms, followed by our LMT miRNA microarray and the Agilent platform.

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Additional file 3:

Supplemental Figure 2: Concordance of matching probes between array platforms. We compared the LMT, Affymetrix FlashTag HSR and Agilent microRNA microarray platforms to one another looking at matching direction of the fold change (up or down). Of the 3 planar microarray platforms, the Affymetrix FlashTag HSR had the highest number of combined up and down regulated miRNA at 111 followed by Agilent with 101 and LMT with 78. Ninety-one, 91, up and down -regulated miRNAs were shared between Agilent and Affymetrix FlashTag HSR, 74 were shared LMT and Affymetrix FlashTag HSR, and 74 were shared between LMT and Agilent.

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Additional file 4:

Supplemental Figure 3: Correlations between miRNA array platforms. To study the correlation of the absolute fold changes between each microarray platform, the fold change data (n = 140) was Log 2 transformed, plotted and the Pearson correlation, r, calculated between platforms (Figure 3). We first compared all of the platforms to our LMT legacy platform to determine which of the commercial platforms correlates best with our reference platform. The Agilent platform demonstrated the highest correlation to our LMT array data (r = 0.882) based on absolute fold change.

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