Comparative expression pathway analysis of human and canine mammary tumors

doi:10.1186/1471-2164-10-135

BMC Genomics
Volume 10

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Uva P
Aurisicchio L
Watters J
Loboda A
Kulkarni A
Castle J
Palombo F
Viti V
Mesiti G
Zappulli V
Marconato L
Abramo F
Ciliberto G
Lahm A
La Monica N
de Rinaldis E

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Uva P
Aurisicchio L
Watters J
Loboda A
Kulkarni A
Castle J
Palombo F
Viti V
Mesiti G
Zappulli V
Marconato L
Abramo F
Ciliberto G
Lahm A
La Monica N
de Rinaldis E
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Research article

Comparative expression pathway analysis of human and canine mammary tumors

Paolo Uva¹ , Luigi Aurisicchio¹ , James Watters² , Andrey Loboda² , Amit Kulkarni³ , John Castle³ , Fabio Palombo¹ , Valentina Viti¹ , Giuseppe Mesiti¹ , Valentina Zappulli⁴ , Laura Marconato⁵ , Francesca Abramo⁶ , Gennaro Ciliberto¹ , Armin Lahm¹ , Nicola La Monica¹ and Emanuele de Rinaldis¹

¹IRBM P. Angeletti, Merck MRL-Rome, Via Pontina Km, 30600 Pomezia, Italy

²Department of Molecular Profiling, Merck Research Laboratories, West Point, Pennsylvania, USA

³Rosetta Inpharmatics LLC, a wholly owned subsidiary of Merck and Co Inc., Terry Avenue North, Seattle, WA 98109, USA

⁴Department of Public Health, Veterinary Hygiene and Comparative Pathology, University of Padua, Italy

⁵Clinica Veterinaria L'Arca, Vico Cacciottoli 46/47, 80129 Naples, Italy

⁶Department of Animal Pathology, University of Pisa, Italy

author email corresponding author email

BMC Genomics 2009, 10:135doi:10.1186/1471-2164-10-135


Published:	27 March 2009

Additional files

Additional file 1:

Description of 33 canine mammary samples. Pathological information and classification (normal, benign, intermediate, malignant) of 33 canine mammary samples extracted from 10 different animals. Malignant mammary tumours were further classified based on the tumour aggressiveness in M1 (infiltrating/solid), M2 (simple) and M3 (complex).

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Additional file 2:

Description of 129 human mammary samples. Information regarding sample classification, tumour size, tumour stage and percentage of tumor cells of the 129 human mammary samples.

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Additional file 3:

List of 1043 group-specific genes selected by ANOVA in dog dataset. – worksheet '1043 AN0VA': genes identified as differentially expressed among the three groups of dog mammary samples (M, malignant; I-B, intermediate-benign; N, normal) (ANOVA, q-value < 0.001). – worksheet 'enrichment analysis': results of the gene set enrichment analysis separately run on each of the six groups identified based on their pattern of expression.

Format: XLS Size: 338KB Download file

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Additional file 4:

Identification of genes most correlated to the 1st principal component and results of gene set enrichment analysis. Results of the gene set enrichment analysis of the genes most correlated to the 1^stprincipal component. The correlations of the genes with the 1^stprincipal component were transformed to SDs from the mean, then genes with values > 1.5 (positive correlation) or < -1.5 (negative correlation) were selected. These genes were analyzed separately by gene set enrichment analysis.

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Additional file 5:

Tumour deregulated genes in human and dog datasets. Genes identified as differentially expressed between tumor and pool of normal samples in human and dog datasets (t-test, q-value < 0.001).

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Additional file 6:

Gene set enrichment analysis of tumor deregulated genes. Results of gene set enrichment analysis of tumor deregulated genes in human and dog. Gene sets that were enriched (p < 0.05) in at least one dataset are shown.

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Additional file 7:

Correlation between prognostic and oncogenic signatures in human breast tumors. Graphical representation of the pair wise Pearson correlation in the human tumor dataset between all the "oncogenic" and "prognostic" signatures described in Table 1. Signatures are ordered by agglomerative hierarchical clustering based on Pearson coefficients.

Format: TIFF Size: 3.1MB Download file

Additional file 8:

Correlation between prognostic and oncogenic signatures in canine mammary tumors. Graphical representation of the pair wise Pearson correlation in the canine tumor dataset between all the "oncogenic" and "prognostic" signatures described in Table 1. Samples are ordered according to the hierarchical clustering computed on human tumors (Additional file 9).

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Additional file 9:

Consent guidelines. Guidelines followed by Genomics Collaborative, Inc. for obtaining patients informed consent.

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Additional file 10:

Consent Module. Informed consent module delivered by Genomics Collaborative, Inc to patients who contributed to the collection human tissue samples.

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Additional file 11:

Log10 of the ratio Tumor vs Pool of Normal for 9,963 dog-human orthologous genes. Contains a tab-delimited file with the normalized log₁₀ratio for the 9,963 dog-human orthologous genes across the 162 samples.

Format: ZIP Size: 8.1MB Download file

Additional file 12:

Error associated to the log10 of the ratio Tumor vs Pool of Normal for 9,963 dog-human orthologous genes. Tab-delimited file with the error associated to the log₁₀ratio for the 9,963 dog-human orthologous genes across the 162 samples.

Format: ZIP Size: 7.4MB Download file

Additional file 13:

Rosetta p-value associated to the log10 of the ratio Tumor vs Pool of Normal for 9,963 dog-human orthologous genes. Tab-delimited file with the Rosetta p-values of differential expression for the 9,963 dog-human orthologous genes across the 162 samples.

Format: ZIP Size: 8.2MB Download file