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Integrating microarray information and using it as a complement to clinicopathological parameters could provide more accurate and robust prognostic tests in order to guide adjuvant systemic treatment that could reduce the cost of breast cancer treatment.
This situation presents a clear and pressing opportunity for the critical examination and ongoing development of methods to: 1) select clinically relevant features from gene expression microarray information; and, 2) use a quantitative measure of those features to define a model which can be used to accurately distinguish between groups of interest e.g., longer versus shorter survival.
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Microarray data and information recommended by the MIAMI (Minimum Information About a MIcroarray experiment) guidelines can be found on the ArrayExpress website [ 6] (Accession number E-MEXP-995 for the independent data set and E-MEXP-979 for the pilot data).
All 501 internal patients and their clinical, pathological and microarray information are tabulated in Table S1 in Additional file 1.
A preliminary database devoted to host Sanger EST information, microarray data and ISH pictures was developed for S. senegalensis [ 19].
Detailed protocols, probe sequences and mappings, gene annotations, all microarray data, and information about the microarray hybridizations are posted on the project website [ 55].
These gene expression changes were compared to microarray information from the Human Ageing Genomic Resources and to the predicted functions of genes in aging or senescence (S4).
The enrichment analyses were made with the total microarray information as the reference set and each sampling time (3 h, 8 h, 24 h, 72 h) and regulation (up or down) as the test sets.
All reporting and depositing of microarray information was conducted per the guidelines of the Minimum Information About a Microarray Experiment (MIAME) [ 15].
For predicting the longer-term clinical response to drug treatment, microarray information could also yield information about possible side effects, and identify markers that, in a clinical context, could be used to predict possible adverse events.
We undertook our analyses using gene expression microarray information from two previously reported studies in separate cancers (melanoma [ 13] and ovarian [ 15]) and utilised PPI information from two different networks (MetaCore™ and iRefWeb [ 50]).
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