  Research articleThe functional landscape of mouse gene expressionWen Zhang1,2* 1 Banting and Best Department of Medical Research, University of Toronto, 1 King's College Circle, Toronto, ON M5S 1A8, Canada 2 Department of Medical Genetics and Microbiology, University of Toronto, 1 King's College Circle, Toronto, ON M5S 1A8, Canada 3 Department of Electrical and Computer Engineering, University of Toronto, 1 King's College Circle, Toronto, ON M5S 1A8, Canada 4 Department of Surgery, University of Toronto, 1 King's College Circle, Toronto, ON M5S 1A8, Canada 5 Samuel Lunenfeld Research Institute, Mount Sinai Hospital, 600 University Avenue, Toronto, ON M5G 1X5, Canada 6 Division of Cell and Molecular Biology, Toronto Western Research Institute and Krembil Neuroscience Center, 399 Bathurst St., Toronto, ON M5T 2S8, Canada 7 The Hospital for Sick Children, 555 University Ave., Toronto, ON M5G 1X8, Canada
Journal of Biology 2004, 3:21doi:10.1186/jbiol16
Additional filesAdditional data file 1: XM (predicted mRNA sequences) from NCBI Format: FA Size: 52.4MB Download file Additional data file 2: XP (encoded protein sequences) from NCBI Format: FA Size: 12.2MB Download file Additional data file 5: Array Master file - 41,699 probes; the Master file contains probe sequences, columns listing the closest sequences in RIKEN, ENSEMBL, Refseq, and Unigene; GenBank description, EST overlap, GO-BP annotations, Domain (most significant) Format: XLS Size: 20MB Download file This file can be viewed with: Microsoft Excel Viewer Additional data file 6: Array information after removal of redundant probes: probe combinations Format: TXT Size: 89KB Download file Additional data file 7: Array information after removal of redundant probes: master file - 39,309 presumed distinct transcripts Format: XLS Size: 20.7MB Download file This file can be viewed with: Microsoft Excel Viewer Additional data file 8: Hybridization records Format: XLS Size: 29KB Download file This file can be viewed with: Microsoft Excel Viewer Additional data file 9: Figure 1 data Format: XLS Size: 101KB Download file This file can be viewed with: Microsoft Excel Viewer Additional data file 10: Figure 2b data Format: XLS Size: 29KB Download file This file can be viewed with: Microsoft Excel Viewer Additional data file 15: Figure 5 data Format: XLS Size: 993KB Download file This file can be viewed with: Microsoft Excel Viewer Additional data file 17: Supplementary figures S1-3 Format: PDF Size: 55KB Download file This file can be viewed with: Adobe Acrobat Reader Additional data file 18: Data: 41,699 probes - single channel, arcsinh intensities Format: ZIP Size: 16.8MB Download file Additional data file 19: Data: 41,699 probes - replicates combined, arcsinh intensities Format: ZIP Size: 9MB Download file Additional data file 20: Data: 41,699 probes - median-subtracted, zeroed Format: ZIP Size: 5.3MB Download file Additional data file 21: Data: 39,309 presumed distinct transcripts - median-subtracted, zeroed Format: ZIP Size: 5MB Download file Additional data file 22: Data: 21,622 presumed distinct transcripts - median-subtracted and zeroed, expressed above 99% of negative-control spots Format: ZIP Size: 2.8MB Download file Additional data file 23: Data: binary matrix of expression above 99% of negative-control spots Format: ZIP Size: 319KB Download file Additional data file 24: Annotations: GO annotations among 39,309 presumed distinct transcripts (12,543 annotated genes, 47,900 annotations) Format: ZIP Size: 202KB Download file Additional data file 25: Annotations: GO annotations among 21,622 presumed distinct transcripts (9,499 annotated genes, 37,876 annotations) Format: ZIP Size: 162KB Download file Additional data file 27: Annotations: map between GO and superGO annotations Format: XLS Size: 73KB Download file This file can be viewed with: Microsoft Excel Viewer Additional data file 28: SVM Predictions: GO-BP SVM Predictions, 15% precision Format: XLS Size: 5.3MB Download file This file can be viewed with: Microsoft Excel Viewer Additional data file 29: SVM Predictions: GO-BP SVM Predictions, 50% precision Format: XLS Size: 529KB Download file This file can be viewed with: Microsoft Excel Viewer Additional data file 30: SVM Predictions: superGO SVM Predictions, 15% precision Format: XLS Size: 3.6MB Download file This file can be viewed with: Microsoft Excel Viewer Additional data file 31: SVM Predictions: superGO SVM Predictions, 50% precision Format: XLS Size: 273KB Download file This file can be viewed with: Microsoft Excel Viewer Additional data file 32: RT-PCR primer sequences Format: XLS Size: 28KB Download file This file can be viewed with: Microsoft Excel Viewer Additional data file 33: XM genes with gene trap lines Format: XLS Size: 1MB Download file This file can be viewed with: Microsoft Excel Viewer Additional data file 34: XM motifs Format: XLS Size: 4.3MB Download file This file can be viewed with: Microsoft Excel Viewer Additional data file 35: 779 known and putative DNA-binding transcription factors among XM genes Format: XLS Size: 137KB Download file This file can be viewed with: Microsoft Excel Viewer Additional data file 36: Table of accession numbers of genes common to Zhang, Su, and Bono data Format: TXT Size: 36KB Download file Additional data file 37: Tech report on spatial detrending Format: PDF Size: 2.2MB Download file This file can be viewed with: Adobe Acrobat Reader Additional data file 38: Map locations of XM genes (BLASTed against Build 32) - retained only if top hit of both XM sequence and array probe overlap (30,387 presumed distinct transcripts) Format: XLS Size: 4.4MB Download file This file can be viewed with: Microsoft Excel Viewer Additional data file 39: SVM functional predictions for 7,147 unannotated mapped transcripts (may be useful for positional cloning), also see [19] Format: XLS Size: 7.5MB Download file This file can be viewed with: Microsoft Excel Viewer Additional data file 40: 175 lists of genes that are expressed in individual tissues, highest in individual tissues, or specific to individual tissues Format: TXT Size: 7.5MB Download file |
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