Open Access Highly Accessed Research article

Exon and junction microarrays detect widespread mouse strain- and sex-bias expression differences

Wan-Lin Su1, Barmak Modrek2, Debraj GuhaThakurta2, Stephen Edwards2, Jyoti K Shah2, Amit V Kulkarni2, Archie Russell2, Eric E Schadt2, Jason M Johnson2 and John C Castle2*

Author Affiliations

1 Molecular and Cellular Biology Program, University of Washington, Seattle, WA 98195, USA

2 Rosetta Inpharmatics LLC, a wholly owned subsidiary of Merck & Co., Inc., 401 Terry Ave N, Seattle, WA 98109, USA

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BMC Genomics 2008, 9:273  doi:10.1186/1471-2164-9-273

Published: 4 June 2008

Additional files

Additional file 1:

Hierarchical clustering of 3' expression profiling dataset. Mouse clustering (agglomerative clustering) based on 3' gene expression profiling.

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Additional file 2:

Correlation between strain-sex groups. Pearson correlation using the average whole transcript profiling log10 ratios from each group.

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Additional file 3:

SNP Analysis. Fisher's exact test for enrichment of probes containing SNPs within differentially expressed probes.

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Additional file 4:

Sex chromosome Analysis. Fisher's exact test for enrichment of differentially expressed probes on the X chromosome.

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Additional file 5:

ANOVA p-values for 3' gene expression profiling dataset. List of genes, raw p-values and Bonferonni-corrected p-values using the 3' gene expression profiling dataset.

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Additional file 6:

ANOVA p-values for whole transcript gene expression profiling dataset. List of genes, raw p-values and Bonferroni-corrected p-values using the whole transcript gene expression profiling dataset.

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Additional file 7:

ANOVA p-values for exon expression profiling dataset. List of genes and associated exons, raw p-values and Bonferroni-corrected p-values using the exon expression profiling dataset.

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Additional file 8:

Analysis of exon probes near splice sites. Fisher's exact test for enrichment of differentially expressed probes within exon probes that overlap with junction probes.

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