Open Access Research article

Drosophila selenophosphate synthetase 1 regulates vitamin B6 metabolism: prediction and confirmation

Kwang Hee Lee12, Myoung Sup Shim1, Jin Young Kim1, Hee Kyoung Jung1, Eunji Lee23, Bradley A Carlson4, Xue-Ming Xu4, Jin Mo Park5, Dolph L Hatfield4, Taesung Park23 and Byeong Jae Lee12*

Author Affiliations

1 Department of Biological Sciences, Seoul National University, Seoul 151-742, Korea

2 Interdisciplinary Program in Bioinformatics, Seoul National University, Seoul 151-742, Korea

3 Department of Statistics, Seoul National University, Seoul 151-742, Korea

4 Laboratory of Cancer Prevention, Center for Cancer Research, National Cancer Institute, National Institutes of Health, Bethesda, MD 20892, USA

5 Department of Dermatology, Massachusetts General Hospital and Harvard Medical School, Boston, MA, 02114, USA

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BMC Genomics 2011, 12:426  doi:10.1186/1471-2164-12-426

Published: 24 August 2011

Additional files

Additional file 1:

List of differentially expressed genes (DEGs). The list of DEGs whose expressions were changed more than 2 fold at least at one time point.

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Additional file 2:

Six Clusters of DEGs and gene-sets used for gene ontology analysis. DEGs were grouped into six clusters and each cluster was classified as one of 3 gene-sets, after box-plotting the DEGs in each cluster. All the DEGs in each gene-set were used for gene ontology analysis.

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Additional file 3:

List of biological process terms selected by GO analysis with three gene-sets. This table is an output obtained by running BinGO software showing genes and their GO biological process terms. The parameters used are described above the table.

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Additional file 4:

Hierarchical structures of GO terms obtained by performing early/down gene-set with different parameters. Panels A and B were examples of hierarchical structures of GO terms obtained by analyzing early/down gene set with BinGO software. They showed similar results, although different parameters were used.

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Additional file 5:

Schematic diagram of vitamin B6 metabolic pathway. The original vitamin B6 metabolic pathway diagram (collected from KEGG database) was modified by indicating DEGs and by showing their expression levels, after SPS1 was knocked down.

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Additional file 6:

Oligonucleotide sequences used as primers for RT-PCR or real-time PCR. List of all oligonucleotides used for RT-PCR and real-time PCR.

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