Metabolomics,Unknown,Transcriptomics,Genomics,Proteomics

Dataset Information

Gene expression profiling of human and dog breast cancers

ABSTRACT: Spontaneous tumors in dog have been demonstrated to share many features with their human counterparts, including relevant molecular targets, histological appearance, genetics, biological behavior and response to conventional treatments. Mammary tumors in dog therefore provide an attractive alternative to more classical mouse models, such as transgenics or xenografts, where the tumour is artificially induced. To assess the extent to which dog tumors represent clinically significant human phenotypes, we performed the first genome-wide comparative analysis of transcriptional changes occurring in mammary tumors of the two species, with particular focus on the molecular pathways involved. Keywords: Expression profiling by array 26 breast tumors and 7 normal mammary glands from dogs. Each sample was hybridized in duplicate with fluor reversal to systematically correct for dye bias. 68 infiltrating ductal mammary carcinoma and 61 adjacent non-involved tissues from humans. Each sample was hybridized in duplicate with fluor reversal to systematically correct for dye bias.

ORGANISM(S): Canis lupus familiaris

SUBMITTER: Emanuele de Rinaldis

PROVIDER: E-GEOD-14999 | biostudies-arrayexpress |

REPOSITORIES: biostudies-arrayexpress

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Publications

Comparative expression pathway analysis of human and canine mammary tumors.

Uva Paolo P Aurisicchio Luigi L Watters James J Loboda Andrey A Kulkarni Amit A Castle John J Palombo Fabio F Viti Valentina V Mesiti Giuseppe G Zappulli Valentina V Marconato Laura L Abramo Francesca F Ciliberto Gennaro G Lahm Armin A La Monica Nicola N de Rinaldis Emanuele E

BMC genomics 20090327

<h4>Background</h4>Spontaneous tumors in dog have been demonstrated to share many features with their human counterparts, including relevant molecular targets, histological appearance, genetics, biological behavior and response to conventional treatments. Mammary tumors in dog therefore provide an attractive alternative to more classical mouse models, such as transgenics or xenografts, where the tumour is artificially induced. To assess the extent to which dog tumors represent clinically signifi ...[more]

PMID: 19327144

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Project description:71 liver RNA samples from three mouse strains - DBA/2J, C57BL/6J and C3H/HeJ - were profiled using a custom-designed microarray monitoring exon and exon-junction expression of 1,020 genes representing 9,406 exons. Gene expression was calculated via two different methods, using the 3'-most exon probe ("3' gene expression profiling") and using all probes associated with the gene ("whole-transcript gene expression profiling"), while exon expression was determined using exon probes and flanking junction probes that spanned across the neighboring exons("exon expression profiling"). Widespread strain and sex influences were detected using a two-way Analysis of Variance (ANOVA) regardless of the profiling method used. However, over 90% of the genes identified in 3' gene expression profiling or whole transcript profiling were identified in exon profiling, along with 75% and 38% more genes, respectively, showing evidence of differential isoform expression. Overall, 55% and 32% of genes, respectively, exhibited strain- and sex-bias differential gene or exon expression. Keywords: Grouped Hybridization material was generated through a random-priming amplification of poly[A]+ purified RNA using primers with a random sequence at the 3' end and a fixed motif at the 5' end that was optimized to generate strand-specific cDNA copies of full-length mRNA transcripts [32]. Since the region used for exon and junction probe selection is constrained to a smaller region, more probes contain sequence with suboptimal characteristics (e.g. high GC content or higher homology to other genes). The hybridization of cDNA, rather than cRNA as commonly done, partially mitigates this issue due to higher specificity and lower background levels [24]. Hybridization conditions were as previously described [33]. All 71 samples were hybridized in a two-channel experiment, where one channel was a common reference, generated by pooling all 71 samples in equal mass. Array hybridizations were done in duplicate with fluor reversal to systematically correct for Cy3/Cy5 dye bias. Array images were processed as described to obtain background noise, single channel intensity and associated measurement error estimates [34]. Expression changes between samples and pool were quantified as mean log10(expression ratio), and associated error.

Dataset Information

Gene expression profiling of human and dog breast cancers

Publications

Comparative expression pathway analysis of human and canine mammary tumors.

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