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This article is part of the supplement: Selected articles from the Tenth Asia Pacific Bioinformatics Conference (APBC 2012)

Open Access Proceedings

miRNA arm selection and isomiR distribution in gastric cancer

Sung-Chou Li12, Yu-Lun Liao3, Meng-Ru Ho1, Kuo-Wang Tsai4, Chun-Hung Lai3 and Wen-chang Lin23*

Author Affiliations

1 Genomics Research Center, Academia Sinica, Taipei, Taiwan

2 Institute of Biomedical Informatics, National Yang-Ming University, Taipei, Taiwan

3 Institute of Biomedical Sciences, Academia Sinica, Taipei, Taiwan

4 Department of Medical Education and Research, Kaohsiung Veterans General Hospital, Kaohsiung, Taiwan

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BMC Genomics 2012, 13(Suppl 1):S13  doi:10.1186/1471-2164-13-S1-S13

Published: 17 January 2012

Additional files

Additional file 1:

The criteria of our mapping procedure. In order to exclude random match, the difference in start position between mature miRNA and mapped reads must be equal to or less than two. While, the difference in end position between mature miRNA and mapped reads must be equal to or less than five.

Format: PDF Size: 43KB Download file

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Open Data

Additional file 2:

The mapping result of all pre-miRNAs in G1245N library. We arranged the miRNA reads from G1245N library within the mapped pre-miRNAs. The read count and location offset of each isomiR are provided.

Format: TXT Size: 596KB Download file

Open Data

Additional file 3:

The mapping result of all pre-miRNAs in G1245N library. We arranged the miRNA reads from G1245T library within the mapped pre-miRNAs. The read count and location offset of each isomiR are provided.

Format: TXT Size: 617KB Download file

Open Data

Additional file 4:

The difficulty in distinguishing nucleotide addition from nucleotide modification. In this case, the last nucleotide variation could be generated from nucleotide modification from C to U at the terminus of the sequence read with 22 nucleotides, which does not alter the length of the read. However, it could also be generated from nucleotide addition of U to the terminus of the read with 21 nucleotides, which lengthens the read by one nucleotide.

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Open Data

Additional file 5:

Inconsistent expression ratios of 5p arm miRNA to 3p arm miRNA. The expression ratios of 5p arm miRNA to 3p arm miRNA are not consistent between gastric normal and gastric tumor tissue, which implies the arm selection preference of 5p arm and 3p arm may varyn between tissues.

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Open Data

Additional file 6:

List of miRNAs whose isomiR distribution patterns significantly differ between normal and tumor tissue. Normal and Tumor denote the expression level of mature miRNA in gastric normal and gastric tumor tissue, respectively. Fold change denote the fold change of miRNA expression level.

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Open Data