Software
Development of a novel data mining tool to find cis-elements in rice gene promoter regions
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* Corresponding author: Shoshi Kikuchi skikuchi@nias.affrc.go.jp
1 National Institute of Agrobiological Sciences, 2-1-2 Kannondai, Tsukuba, Ibaraki 305-8602, Japan
2 Hitachi Software Engineering Japan Co., Ltd., 6-81 Onoe-cho, Naka-ku, Yokohama 231-0015, Japan
3 International Rice Research Institute, DAPO 7777, Metro Manila, Philippines
BMC Plant Biology 2008, 8:20 doi:10.1186/1471-2229-8-20
Published: 27 February 2008Additional files
Additional file 1:
Known plant cis-elements listed for analysis by RiCES. See text for further details.
Format: XLS Size: 104KB Download file
This file can be viewed with: Microsoft Excel Viewer
Additional file 2:
Transcription units (TUs) used in the feasibility test. Auxin-inducible genes were picked up from RiceTFDB 2.0 (1st column). Corresponding full-length cDNAs were designated by BLASTN (2nd column) and translated to TUs defined in Pseudomolecule ver. 4 (3rd column).
Format: CSV Size: 2KB Download file
Additional file 3:
Preliminary list of cis-element candidates listed by MEME analysis for TUs shown in Supplementary Table S2. See text for further details.
Format: TXT Size: 61KB Download file
Additional file 4:
Result of association rule analysis of cis-element candidates listed by MEME. 1st column: examined sequence. 2nd column: number of TUs possessing the designated motif within 28 TUs of the target gene list. 3rd column: number of TU possessing the designated motif within 22 943 TUs stored in KOME database. 4th column: lift value.
Format: CSV Size: 100KB Download file
Additional file 5:
Result of sequence search for motifs shown in Supplementary Table S1 in 22 943 TUs stored in KOME database. 1st column: examined TUs. 2nd column: motifs found in upstream region of TU. Other columns: position of motifs within the upstream region of each TU.
Format: CSV Size: 467KB Download file
Additional file 6:
Result of association rule analysis after sequence search shown in Supplementary Table S6. 1st column: examined sequence. 2nd column: number of TUs possessing the designated motif within 28 TUs of the target gene list. 3rd column: number of TU possessing the designated motif within 22 943 TUs stored in KOME database. 4th column: lift value.
Format: CSV Size: 1KB Download file