  Research articleThe functional landscape of mouse gene expressionWen Zhang* 1,2 1Banting and Best Department of Medical Research, University of Toronto, 1 King's College Circle, Toronto, ON M5S 1A8, Canada 2Department of Medical Genetics and Microbiology, University of Toronto, 1 King's College Circle, Toronto, ON M5S 1A8, Canada 3Department of Electrical and Computer Engineering, University of Toronto, 1 King's College Circle, Toronto, ON M5S 1A8, Canada 4Department of Surgery, University of Toronto, 1 King's College Circle, Toronto, ON M5S 1A8, Canada 5Samuel Lunenfeld Research Institute, Mount Sinai Hospital, 600 University Avenue, Toronto, ON M5G 1X5, Canada 6Division of Cell and Molecular Biology, Toronto Western Research Institute and Krembil Neuroscience Center, 399 Bathurst St., Toronto, ON M5T 2S8, Canada 7The 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: 53.7MB Download file Additional data file 2: XP (encoded protein sequences) from NCBI Format: FA Size: 12.5MB 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: 20.5MB 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: 21.2MB 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: 17.2MB Download file Additional data file 19: Data: 41,699 probes - replicates combined, arcsinh intensities Format: ZIP Size: 9.2MB Download file Additional data file 20: Data: 41,699 probes - median-subtracted, zeroed Format: ZIP Size: 5.4MB Download file Additional data file 21: Data: 39,309 presumed distinct transcripts - median-subtracted, zeroed Format: ZIP Size: 5.1MB 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: 5.5MB 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: 3.7MB 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: 4.4MB 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: 4.5MB 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: 7.7MB 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: 7.7MB Download file |
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