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Previously unidentified changes in renal cell carcinoma gene expression identified by parametric analysis of microarray data

Marc E Lenburg1, Louis S Liou2, Norman P Gerry1, Garrett M Frampton1, Herbert T Cohen3 and Michael F Christman1*

  • * Corresponding author: Michael F Christman mfc@bu.edu

Author Affiliations

1 Departments of Genetics & Genomics, Boston University School of Medicine 715 Albany Street, E613 Boston, Massachusetts 02118, USA

2 Urology, Boston University School of Medicine 715 Albany Street, E613 Boston, Massachusetts 02118, USA

3 Medicine, Boston University School of Medicine 715 Albany Street, E613 Boston, Massachusetts 02118, USA

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BMC Cancer 2003, 3:31  doi:10.1186/1471-2407-3-31

Published: 27 November 2003

Additional files

Additional File 1:

Tab-delimited text file (1 KB) listing the genes >3.0 fold changed in RCC that are identified by the paired-sample t-test with p < 0.03 and are not also identified by the unpaired t-test. Columns include: the Affymetrix probeset ID, the gene symbol, a descriptive title, the genbank accession of the sequence which was used in the design of the probeset, the -log10 p-value of the paired-sample t-test, and the log2 of the ratio of the geometric mean tumor intensity to the geometric mean adjacent normal tissue intensity.

Format: TXT Size: 1KB Download file

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Additional File 2:

Tab-delimited text file (345 KB) listing all the probesets > 3.0 fold changed in RCC that are identified by the unpaired t-test with p < 0.03. Columns include: the Affymetrix probeset ID, the genbank accession of the sequence which was used in the design of the probeset, the gene symbol, a descriptive title, the cytologic map position of the gene, the unigene cluster ID, the gene ontology biological process ID, the gene ontology cellular component ID, the gene ontology molecular function ID, the -log10 p-value of the paired-sample t-test, the log2 of the ratio of the geometric mean tumor intensity to the geometric mean adjacent normal tissue intensity, whether the probeset had a paired t-test p < 0.03, whether there are multiple probesets with sequence-specific hybridization for this unigene cluster, whether any additional probesets are < 3.0 fold changed or have a t-test p > 0.03 (column labeled "heterogeneous"), and whether the average fold-change and t-test p-value meet our criteria for differential expression (column labeled "kept in final list").

Format: TXT Size: 354KB Download file

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Additional File 3:

Tab-delimited text file (196 KB) listing all the probesets that map to a unigene cluster for which there is at least one probeset with a > 3.0 fold change in RCC and an unpaired t-test with p < 0.03 and at least one additional probeset with a < 3.0 fold change or t-test p > 0.03. Columns include: the Affymetrix probeset ID, a descriptive title, the gene symbol, the cytologic map position of the gene, the genbank accession of the sequence which was used in the design of the probeset, the unigene cluster ID, the gene ontology biological process ID, the gene ontology cellular component ID, the gene ontology molecular function ID, the -log10 p-value of the paired-sample t-test, the log2 of the ratio of the geometric mean tumor intensity to the geometric mean adjacent normal tissue intensity, whether the probeset has a > 3.0 fold change in RCC and an unpaired t-test with p < 0.03.

Format: TXT Size: 196KB Download file

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Additional File 4:

Adobe portable document file (PDF, 36 KB) listing the subset of genes differentially expressed in RCC that are associated with the keywords hypoxia, angiogenesis, tnf, apoptosis, interferon, resistance, metastasis, and kidney.

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This file can be viewed with: Adobe Acrobat Reader

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