  Research articleComparative BAC end sequence analysis of tomato and potato reveals overrepresentation of specific gene families in potatoErwin Datema1,2 1Applied Bioinformatics, Plant Research International, PO Box 16, 6700 AA, Wageningen, The Netherlands 2Laboratory of Bioinformatics, Wageningen University, Transitorium, Dreijenlaan 3, 6703 HA Wageningen, The Netherlands 3Department of Plant Breeding and Genetics, Cornell University, Ithaca, New York 14853, USA 4United States Department of Agriculture and Boyce Thompson Institute for Plant, Research, Cornell University, Ithaca, New York 14853, USA 5Laboratory of Plant Breeding, Wageningen University, P.O. Box 386, 6700 AJ Wageningen, The Netherlands 6Centre for BioSystems Genomics (CBSG), PO Box 98, 6700 AB Wageningen, The Netherlands
BMC Plant Biology 2008, 8:34doi:10.1186/1471-2229-8-34
Additional filesAdditional file 1: This file describes the keyword filtering that has been applied after the BLASTX searches to the non-redundant protein database, in order to distinguish between true putative protein-coding regions, and repetitive and/or contamination-related sequences. Format: DOC Size: 33KB Download file This file can be viewed with: Microsoft Word Viewer Additional file 2: This file describes the Gene Ontology terms found in the InterProScan analysis of the tomato and potato EcoRI digested BAC end sequences. The columns in this Table describe the GO term, the number of BAC end sequences in the tomato Eco and potato PPT library that had this term assigned to them, and the P value of Fisher's exact test for the difference of relative abundance of this GO term between these two libraries. A P value lower than 10-4 indicates a significant difference in the abundance of a GO term between these libraries. Format: XLS Size: 57KB Download file This file can be viewed with: Microsoft Excel Viewer Additional file 3: This file describes the Gene Ontology terms found in the InterProScan analysis of the tomato and potato HindIII digested BAC end sequences. The columns in this Table describe the GO term, the number of BAC end sequences in the tomato HBa and potato POT library that had this term assigned to them, and the P value of Fisher's exact test for the difference of relative abundance of this GO term between these two libraries. A P value lower than 10-4 indicates a significant difference in the abundance of a GO term between these libraries. Format: XLS Size: 73KB Download file This file can be viewed with: Microsoft Excel Viewer Additional file 4: This file describes the Gene Ontology terms found in the InterProScan analysis of the potato HindIII and EcoRI digested BAC end sequences. The columns in this Table describe the GO term, the number of BAC end sequences in the potato POT and PPT library that had this term assigned to them, and the P value of Fisher's exact test for the difference of relative abundance of this GO term between these two libraries. A P value lower than 10-4 indicates a significant difference in the abundance of a GO term between these libraries. Format: XLS Size: 67KB Download file This file can be viewed with: Microsoft Excel Viewer Additional file 5: This file describes the Gene Ontology terms found in the InterProScan analysis of the tomato HindIII and EcoRI digested BAC end sequences. The columns in this Table describe the GO term, the number of BAC end sequences in the tomato HBa and Eco library that had this term assigned to them, and the P value of Fisher's exact test for the difference of relative abundance of this GO term between these two libraries. A P value lower than 10-4 indicates a significant difference in the abundance of a GO term between these libraries. Format: XLS Size: 68KB Download file This file can be viewed with: Microsoft Excel Viewer Additional file 6: This file describes the PANTHER families found in the InterProScan analysis of the tomato and potato EcoRI digested BAC end sequences. The columns in this Table describe the PANTHER family, the number of BAC end sequences in the tomato Eco and potato PPT library that had this term assigned to them, and the P value of Fisher's exact test for the difference of relative abundance of this GO term between these two libraries. A P value lower than 10-4 indicates a significant difference in the abundance of a GO term between these libraries. Format: XLS Size: 93KB Download file This file can be viewed with: Microsoft Excel Viewer Additional file 7: This file describes the PANTHER families found in the InterProScan analysis of the tomato and potato HindIII digested BAC end sequences. The columns in this Table describe the PANTHER family, the number of BAC end sequences in the tomato HBa and potato POT library that had this term assigned to them, and the P value of Fisher's exact test for the difference of relative abundance of this GO term between these two libraries. A P value lower than 10-4 indicates a significant difference in the abundance of a GO term between these libraries. Format: XLS Size: 124KB Download file This file can be viewed with: Microsoft Excel Viewer Additional file 8: This file describes the PANTHER families found in the InterProScan analysis of the potato HindIII and EcoRI digested BAC end sequences. The columns in this Table describe the PANTHER family, the number of BAC end sequences in the potato POT and PPT library that had this term assigned to them, and the P value of Fisher's exact test for the difference of relative abundance of this GO term between these two libraries. A P value lower than 10-4 indicates a significant difference in the abundance of a GO term between these libraries. Format: XLS Size: 110KB Download file This file can be viewed with: Microsoft Excel Viewer Additional file 9: This file describes the PANTHER families found in the InterProScan analysis of the tomato HindIII and EcoRI digested BAC end sequences. The columns in this Table describe the PANTHER family, the number of BAC end sequences in the tomato HBa and Eco library that had this term assigned to them, and the P value of Fisher's exact test for the difference of relative abundance of this GO term between these two libraries. A P value lower than 10-4 indicates a significant difference in the abundance of a GO term between these libraries. Format: XLS Size: 113KB Download file This file can be viewed with: Microsoft Excel Viewer |
|
|
|
 |  | Log on / register Feedback | Support | My details |
on Google Scholar
author email
corresponding author email|
|
| © 1999-2008 BioMed Central Ltd unless otherwise stated |