Open Access Highly Accessed Research article

The functional landscape of mouse gene expression

Wen Zhang12, Quaid D Morris13, Richard Chang1, Ofer Shai3, Malina A Bakowski1, Nicholas Mitsakakis1, Naveed Mohammad1, Mark D Robinson1, Ralph Zirngibl2, Eszter Somogyi2, Nancy Laurin2, Eftekhar Eftekharpour4, Eric Sat5, Jörg Grigull1, Qun Pan1, Wen-Tao Peng1, Nevan Krogan12, Jack Greenblatt12, Michael Fehlings46, Derek van der Kooy2, Jane Aubin2, Benoit G Bruneau27, Janet Rossant25, Benjamin J Blencowe12, Brendan J Frey3 and Timothy R Hughes12*

Author Affiliations

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

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Journal of Biology 2004, 3:21  doi:10.1186/jbiol16

Published: 6 December 2004

Additional files

Additional data file 1:

XM (predicted mRNA sequences) from NCBI

Format: FA Size: 52.4MB Download file

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Additional data file 2:

XP (encoded protein sequences) from NCBI

Format: FA Size: 12.2MB Download file

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Additional data file 3:

Array Design 1 (spot map)

Format: TDT Size: 2MB Download file

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Additional data file 4:

Array Design 2 (spot map)

Format: TDT Size: 2MB Download file

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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

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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 11:

Figure 4a data

Format: ZIP Size: 2.6MB Download file

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Additional data file 12:

Figure 4b data

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Additional data file 13:

Figure 4c data

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Additional data file 14:

Figure 4d data

Format: TXT Size: 27KB Download file

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Additional data file 15:

Figure 5 data

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Additional data file 16:

Figure 7 data

Format: TXT Size: 516KB 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

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Additional data file 19:

Data: 41,699 probes - replicates combined, arcsinh intensities

Format: ZIP Size: 9MB Download file

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Additional data file 20:

Data: 41,699 probes - median-subtracted, zeroed

Format: ZIP Size: 5.3MB Download file

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Additional data file 21:

Data: 39,309 presumed distinct transcripts - median-subtracted, zeroed

Format: ZIP Size: 5MB Download file

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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

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Additional data file 23:

Data: binary matrix of expression above 99% of negative-control spots

Format: ZIP Size: 319KB Download file

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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

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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

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Additional data file 26:

Annotations: superGO annotations

Format: ZIP Size: 88KB Download file

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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

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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

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