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miRExpress: Analyzing high-throughput sequencing data for profiling microRNA expression

Wei-Chi Wang1, Feng-Mao Lin1, Wen-Chi Chang15, Kuan-Yu Lin23, Hsien-Da Huang14* and Na-Sheng Lin23*

Author Affiliations

1 Institute of Bioinformatics and Systems Biology, National Chiao Tung University, Hsin-Chu 300, Taiwan, Republic of China

2 Institute of Biotechnology, National Cheng Kung University, Tainan 701, Taiwan, Republic of China

3 Institute of Plant and Microbial Biology, Academia Sinica, Nankang, Taipei 11529, Taiwan, Republic of China

4 Department of Biological Science and Technology, National Chiao Tung University, Hsin-Chu 300, Taiwan, Republic of China

5 Institute of Tropical Plant Science, National Cheng Kung University, Tainan 701, Taiwan, Republic of China

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BMC Bioinformatics 2009, 10:328  doi:10.1186/1471-2105-10-328

Published: 12 October 2009

Additional files

Additional file 1:

miRNA expressions profile in Arabidopsis. Arabidopsis miRNA expression profile in three experimental conditions

Format: XLS Size: 34KB Download file

This file can be viewed with: Microsoft Excel Viewer

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Additional file 2:

miRNA expressions profile in human embryonic stem cells. Human embryonic stem cells miRNA expression profile in two experimental conditions

Format: XLS Size: 25KB Download file

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Additional file 3:

Novel miRNA candidate expression profiles in human embryonic stem cells. Using cross-species known miRNAs to construct novel miRNA candidate expression profiles in human embryonic stem cells

Format: XLS Size: 21KB Download file

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Open Data

Additional file 4:

Read number distributions between miRExpress and Fasteris. Comparison of read number distributions obtained using miRExpress and Fasteris. The correlation coefficients of read number distribution in Mock, BaMV and BaMV+BSF4 are 0.999, 0.998 and 0.996, respectively.

Format: PNG Size: 146KB Download file

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Additional file 5:

Read count distributions between miRExpress and Fasteris. Comparison of read count distributions obtained using miRExpress and Fasteris. Correlation coefficients of read number distribution in Mock, BaMV and BaMV+BSF4 are 0.997, 0.996 and 0.986, respectively.

Format: PNG Size: 231KB Download file

Open Data

Additional file 6:

Compare miRNA expressions profile in Arabidopsis between miRExpress and aligning reads to genome. Compare Arabidopsis miRNA expression profile in three experimental conditions by different methods. One is miRExpress. Another is aligning sequence to genome.

Format: XLS Size: 35KB Download file

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Additional file 7:

miRNA expressions profile in human embryonic stem cells between miRExpress and Morin et al. Compare human embryonic stem cell miRNA expression profile in two experimental conditions by different methods. One is miRExpress. Another is Morin et al.

Format: XLS Size: 25KB Download file

This file can be viewed with: Microsoft Excel Viewer

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Additional file 8:

Spending time in constructing miRNA expression profiles between miRExpress and blast. The data sets of three experimental conditions in Arabidopsis are used to compare spending time in constructing miRNA expression profiles between miRExpress and blast.

Format: XLS Size: 17KB Download file

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Open Data