Research article
The functional landscape of mouse gene expression
- † Equal contributors
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, 3:21 doi:10.1186/jbiol16
Published: 6 December 2004Additional files
Additional 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
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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
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Additional data file 8:
Hybridization records
Format: XLS Size: 29KB Download file
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Additional data file 9:
Figure 1 data
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Additional data file 10:
Figure 2b data
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Additional data file 15:
Figure 5 data
Format: XLS Size: 993KB Download file
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Additional data file 17:
Supplementary figures S1-3
Format: PDF Size: 55KB Download file
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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
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Additional data file 28:
SVM Predictions: GO-BP SVM Predictions, 15% precision
Format: XLS Size: 5.3MB Download file
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Additional data file 29:
SVM Predictions: GO-BP SVM Predictions, 50% precision
Format: XLS Size: 529KB Download file
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Additional data file 30:
SVM Predictions: superGO SVM Predictions, 15% precision
Format: XLS Size: 3.6MB Download file
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Additional data file 31:
SVM Predictions: superGO SVM Predictions, 50% precision
Format: XLS Size: 273KB Download file
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Additional data file 32:
RT-PCR primer sequences
Format: XLS Size: 28KB Download file
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Additional data file 33:
XM genes with gene trap lines
Format: XLS Size: 1MB Download file
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Additional data file 34:
XM motifs
Format: XLS Size: 4.3MB Download file
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Additional data file 35:
779 known and putative DNA-binding transcription factors among XM genes
Format: XLS Size: 137KB Download file
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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
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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
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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
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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
