Embedding R in Windows applications, and executing R remotely

Comparative analysis of the oes t r o g e n- responsive gene expression profile o f breast cancer cells
with three different microarray platforms
M a r g h e r i t a M u t a r e l l i ( 1 ) , ( 2 ) , W a l t e r B a s i l e ( 3 ) , Luigi Cicatiello ( 3 ) , Claudio Scafoglio ( 3 ) , Giovanni Colonna ( 2 ) , A l e s s a n d r o
W e i s z ( 3 ) A n g e l o F a c c h i a n o (1),(2)
1 Istituto di Scienze dell’Alimentazione CNR, via Roma 52A/C, 83100 Avellino
2 Centro di Ricerca Interdipartimentale di Scienze Computazionali e Biotecnologiche, Seconda Università degli Studi di
N a p o l i , v i a d e C r e c c h i o , 8 0 1 3 8 N a p o l i , I t a l y
3
Dipartimento di Patologia Generale, Seconda Università degli Studi di Napoli, via de Crecchio, 80138 Napoli
The DNA microarray i s a technique which makes it possible to analyze the expression patterns of tens
of thousands genes in a short time . The widespread use of this technique and the rapidl y improving
different technologies available by commercial and academic providers has led to the publication of
thousands of results, extremely heterogeneous in terms of technology used and analysis subsequently
applied to data. This leads to a difficulty in collaborating and exchange data between groups with
common research interest, whereas collaboration s would be extremely useful due to the high cost of
this techniques and to the consideration that an experiment carefully designed could bring results
relevant to different groups, each focusing on a different aspect of a main biological problem. So the
awareness for the need of common standards or, at least , comparable technologies is emerging in the
scientific community, as shown by the effort of the Microarray Gene Expression Data (MGED)
S o c i e t y, which is trying to set up at least experimental methodology, ontology and data format
standards .
In addition, it is important the ability of being able to compare newly produced data with preceding
experiments, so to ensure of keeping high t h e value of results produced with equipment of the old
generation.
We thus started this work with the aim of evaluating the technical variability between three
commonly used microarray platfo rms, such to adapt the first part of the analysis to the peculiarity of
each technique, and the feasibility of a common subsequent analysis path, thus taking advantage of the
different data-extraction abilities of the three. The chips used to study the gene expression profiles of
hormone -responsive breast cancer cells with and without stimulation with estradiol are:
i ) the Incyte ‘UniGEM V 2.0’ microarrays, containing over 14,000 PCR- amplified cDNAs,
corresponding to 8286 unique genes, spotted at a high density pattern onto glass slides ;
ii) the Affymetrix technology, based on 25 nucleotide-long oligonucleotides directly
synthesized on a GeneChip® array, representing more than 39,000 transcripts derived from
approximately 33,000 unique human genes;
iii) the Agilent ‘Human 1A Oligo’ Microarray consisting of 60-mer, i n s i t u synthesized
oligonucleotide probes for a total of about 18000 different genes.
The same samples were used to generate fluorescent targets to be hyb ridized on the different slides ,
w i t h balanced dye swap when applicable for competitive hybridizations.
Ackowledgements
R e s e a r c h s u p p o r t e d b y : I t a l i a n A s s o c i a t i o n f o r C a n c e r R e s e a r c h ( A I R C , I n v e s t i g a t o r G r a n t s 2 0 0 3 ) , I t a l i a n M i n i s t r y f o r
Education, University and Research: FIRB Post -genomica (Grant RBNE0157EH_001/_003), European Commission
(Contract BMH4 -C T 9 8 -3433), Ministry of Health (Progetti Speciali 2000 and RF02/184), Second University of Naples
( R i c e r c a d i A t e n e o 2 0 0 2 -2 0 0 3 ). M . M u t a r e l l i a nd C . S c a f o g l i o a r e P h D s tu d e n t s , supported by EU funds, of Dottorato di
Ricerca in “Biologia Computazionale” and in “Oncologia medica e chirurgica ed Immunologia clinica”, respectively, at the
S e c o n d U n i v e r s i t y o f N a p l e s .