This article is part of the supplement: APBioNet – Fifth International Conference on Bioinformatics (InCoB2006)
Proceedings
Computational promoter analysis of mouse, rat and human antimicrobial peptide-coding genes
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* Corresponding authors: Christian Schönbach schoen@ntu.edu.sg - Vladimir B Bajic vlad@sanbi.ac.za
- † Equal contributors
1 Knowledge Extraction Laboratory, Institute for Infocomm Research, 21 Heng Mui Keng Terrace, Singapore 119613, Singapore
2 Department of Biochemistry, Faculty of Medicine, National University of Singapore, 8 Medical Drive, Singapore 117597, Singapore
3 Immunoinformatics Research Team, Advanced Genome Information Technology Group, RIKEN Genomic Sciences Center (GSC), RIKEN Yokohama Institute, 1-7-22 Suehiro-cho, Tsurumi-ku, Yokohama, Kanagawa, 230-0045, Japan
4 Division of Genomics and Genetics, School of Biological Sciences, Nanyang Technological University, Singapore 637551, Singapore
5 Department of Obstetrics and Gynecology, National University Hospital, National University of Singapore, 5 Lower Kent Ridge Road, Singapore 119074, Singapore
6 University of the Western Cape, South African National Bioinformatics Institute (SANBI), Private Bag X17, Bellville 7535, South Africa
7 Brigham Young University, Department of Microbiology and Molecular Biology, 753 WIDB, Provo, UT 84602, USA
8 ARC Special Research Centre for Functional and Applied Genomics, Institute for Molecular Bioscience, The University of Queensland, Brisbane, Queensland 4072, Australia
9 Genome Exploration Research Group (Genome Network Project Core Group), RIKEN Genomic Sciences Center (GSC), RIKEN Yokohama Institute, 1-7-22 Suehiro-cho, Tsurumi-ku, Yokohama, Kanagawa, 230-0045, Japan
10 Genome Science Laboratory, Discovery Research Institute, RIKEN Wako Institute, 2-1 Hirosawa, Wako, Saitama, 351-0198, Japan
BMC Bioinformatics 2006, 7(Suppl 5):S8 doi:10.1186/1471-2105-7-S5-S8
Published: 18 December 2006Additional files
Additional file 2:
Supplementary table 2. AMPeg families and representative members in mouse, rat and human.
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Additional file 3:
Supplementary table 3. TFs associated with ab initio-predicted TFBSs that coincided with experimental data.
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Additional file 4:
Supplementary table 4. Over-represented motifs that are common in multiple AMP families.
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Additional file 5:
Supplementary tables 5A and 5B Distribution of motifs corresponding to different TF groups among AMP families and Ranking of TF groups according to their frequency of appearance in different AMP families.
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Additional file 6:
Supplementary table 6. Distribution of individual transcription factors among AMP families.
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Additional file 7:
Supplementary table 7. Common motifs detected among groups of enteris and myeloid-specific alpha-defensins.
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Additional file 8:
Supplementary table 8. Motif distribution across the rat Defcr4, Defa6, Defa8 and Defa9 promoter regions.
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Additional file 9:
Supplementary tables 9A and 9B. TF binding sites that correspond to ab initio-predicted motifs derived from the Penk family promoter regions and Motif arrangements in promoter region in mouse (4922504O09), human (HIX0007519.2) and rat (NM_017139) of Penk family members.
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Additional file 10:
Supplementary tables 10A and 10B. TF binding sites that correspond to ab initio-predicted motifs derived frokm Zap family promoter regions and Promoter motif arrangements in mouse (FA20004O17), human (HIX0007129.3) and rat (NM_173045) Zap family members.
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Additional file 11:
Supplementary table 11. P-value table of motif groups.
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Additional file 1:
Supplementary table 1. FANTOM3 dataset-derived AMP transcripts which were new to mouse and absent in human.
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