Development of a novel data mining tool to find cis-elements in rice gene promoter regions

Koji Doi¹ , Aeni Hosaka¹ , Toshifumi Nagata¹ , Kouji Satoh¹ , Kohji Suzuki² , Ramil Mauleon³ , Michael J Mendoza³ , Richard Bruskiewich³ and Shoshi Kikuchi¹

¹National Institute of Agrobiological Sciences, 2-1-2 Kannondai, Tsukuba, Ibaraki 305-8602, Japan

²Hitachi Software Engineering Japan Co., Ltd., 6-81 Onoe-cho, Naka-ku, Yokohama 231-0015, Japan

³International Rice Research Institute, DAPO 7777, Metro Manila, Philippines

author email corresponding author email

BMC Plant Biology 2008, 8:20doi:10.1186/1471-2229-8-20


Published:	27 February 2008

Additional files

Additional file 1:

Known plant cis-elements listed for analysis by RiCES. See text for further details.

Format: XLS Size: 104KB Download file

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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).

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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