Research
Genome-wide review of transcriptional complexity in mouse protein kinases and phosphatases
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* Corresponding author: Alistair RR Forrest a.forrest@imb.uq.edu.au
1 Institute for Molecular Bioscience and ARC Centre in Bioinformatics, University of Queensland, Brisbane, QLD 4072, Australia
2 Queensland Institute for Medical Research, PO Royal Brisbane Hospital, Brisbane, QLD 4029, Australia
3 Center for Genomics and Bioinformatics, Karolinska Institutet, S-171 77 Stockholm, Sweden
4 Genome Exploration Research Group (Genome Network Project Core Group), RIKEN Genomic Sciences Center (GSC), RIKEN Yokohama Institute, Yokohama, Kanagawa, 230-0045, Japan
5 The Eskitis Institute for Cell and Molecular Therapies, Griffith University, QLD 4111, Australia
6 Genome Science Laboratory, Discovery Research Institute, RIKEN Wako Institute, Wako, Saitama, 351-0198, Japan
Genome Biology 2006, 7:R5 doi:10.1186/gb-2006-7-1-r5
Published: 26 January 2006Additional files
Additional data file 1:
An Excel file listing all protein kinase-like and protein phosphatase-like loci considered in this study (sheet 1 lists the 522 kinase-like and 158 phosphatase-like loci with detected transcripts; sheets 2 and 3 provide details of the entries retired because of false positives, and duplications in reported by Forrest [22] and Caenepeel [23] and their coworkers; and sheet 4 provides a list of predicted transcripts still awaiting confirmation by cDNA evidence).
Format: XLS Size: 264KB Download file
This file can be viewed with: Microsoft Excel Viewer
Additional data file 2:
A pdf file containing a pair of screen captures demonstrating visualization of the Araf and Dcamkl1 protein kinase loci (note alternative well supported 5' and 3' exons that structurally divide the loci).
Format: PDF Size: 125KB Download file
This file can be viewed with: Adobe Acrobat Reader
Additional data file 3:
An Excel file listing alternative splice junctions identified in the set and the cDNA accession numbers that support them.
Format: XLS Size: 5.9MB Download file
This file can be viewed with: Microsoft Excel Viewer
Additional data file 4:
A zip file containing four Excel files (5' exon, 3' exon, TSS and TTS clusters).
Format: ZIP Size: 1.1MB Download file
Additional data file 5:
A zip file containing a PowerPoint presentation with genomic views of the 5'-RACE results and an Excel file summarizing the results and the primer sequences used.
Format: ZIP Size: 745KB Download file
Additional data file 6:
An Excel file of zinc finger loci with levels of support for alternative transcripts.
Format: XLS Size: 199KB Download file
This file can be viewed with: Microsoft Excel Viewer
Additional data file 7:
An Excel file that contains supporting evidence for the variant receptors discussed in the results, providing links to MPSS, GNF, and CAGE for transcriptional evidence, links into PubMed for known examples, and other supporting evidence.
Format: XLS Size: 69KB Download file
This file can be viewed with: Microsoft Excel Viewer
Additional data file 8:
A pdf file containing a listing of clones predicted as NMD candidates.
Format: PDF Size: 62KB Download file
This file can be viewed with: Adobe Acrobat Reader
Additional data file 9:
An Excel file containing the domain combinations, complements, and raw Interpro results for all full-length transcripts in the phosphoregulator set.
Format: XLS Size: 5.4MB Download file
This file can be viewed with: Microsoft Excel Viewer
Additional data file 10:
A pdf file showing a graph of the number of loci with alternative splice junctions, and 5' terminal or 3' terminal exons (for a junction to be considered variant it requires two independent cDNAs - one cDNA flags the sequence as potential; for terminal exons a count of five events is required for it to be considered variant - two events flag the sequence as potential).
Format: PDF Size: 6KB Download file
This file can be viewed with: Adobe Acrobat Reader
Additional data file 11:
An Excel file summarizing the predicted domain combination and variant type for the 1473 full-length ORFs identified in the domain structure analysis.
Format: XLS Size: 1.6MB Download file
This file can be viewed with: Microsoft Excel Viewer
Additional data file 12:
A zip file containing an Excel file summarizing the quantitative real-time PCR results for the Csf1r receptor variants and a pdf file containing additional localization images for the secreted isoform.
Format: ZIP Size: 784KB Download file