Transcriptional profiling of Drosophila neoplastic tumors to identify Ets21C dependent target genes
Ontology highlight
ABSTRACT:
ORGANISM(S): Drosophila melanogaster
SUBMITTER: Janine Toggweiler
PROVIDER: E-MTAB-4315 | biostudies-arrayexpress |
REPOSITORIES: biostudies-arrayexpress
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Chips were scanned, and hybridization data were acquired using Affymetrix Suite 5.0 software. Affymetrix CEL files were normalized and quantified using Bioconductor software with the gcRMA model to quantify gene expression levels (Gentleman and Carey, 2002). Unsupervised principal components analysis (PCA) was used to identify the relationships among normal adult cerebellum, GCPs, pre-neoplastic cells and tumor cells based on expression profiles. To identify genes that were differentially expressed among GCPs, pre-neoplastic cells and tumor cells, supervised analysis was carried out. A gene-by-gene ANOVA model with three groups (GCP, pre-neoplastic, tumor) was used to fit the log2-transformed intensities. To correct for multiple comparisons, the nominal p-value was adjusted using the false discovery rate (Benjamini and Hochberg, 1995). Genes were considered to be differentially expressed if they satisfied all of the following criteria: a difference in expression greater than 1.9-fold between any two groups, a maximum absolute intensity difference larger than 32 units, and an adjusted pvalue < 0.01. There were 118 genes that met these criteria. The identities of differentially expressed genes were verified by integrating data from the Affymetrix and Unigene databases. Gene functions were determined using information from Gene Ontology, Unigene, LocusLink and PubMed databases. Clustering was performed with Cluster and Treeview (Eisen et al., 1998). All statistical analysis was performed using R-1.7 software (Dalgaard, 2002). Results were visualized with Spotfire 6.0 (Somerville, MA). CORRESPONDING AUTHOR; Robert J. Wechsler-Reya*; Dept. of Pharmacology & Cancer Biology,; Duke University Medical Center Box 3813, Durham, NC 27710; Phone: 919-613-8754. Fax: 919-668-3556. Email: rw.reya@duke.edu; SUBMITTER_CITATION: Oliver TG, Read TA. Kessler JS, Mehmeti A, Wekks JF, Huynh TT, Lin SM, Wechsler-Reya RJ, Loss of patched and disruption of granule cell development in a pre-neoplastic stage of medulloblastoma, Development, 132, 2425-2439 (2005)
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