Computational protocol: Gene profiling of the erythro- and megakaryoblastic leukaemias induced by the Graffi murine retrovirus

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Protocol publication

[…] Data Set Normalization: Affymetrix MicroArray Suite version 5.0 was used to scan and quantify the arrays. Normalization of gene expression data were performed using the Bioconductor implementation of RMA (Robust Multi Array, B. Bolstad, University of California, Berkeley) available from the Flexarray software (1.2, R 2.7.2, []).Unsupervised learning: Hierarchical clustering (complete linkage clustering, correlation uncentered, []) and Self-Organization Maps (SOM, parameters G 1-5, A 1-10, []) were constructed using GeneCluster software (M. Eisen). 3,000 transcripts were selected to be included in the analyses based on the differential expression from the mean. The deviation from the mean was calculated from the RMA values of the 45,000 probesets and the data were ranked in decreasing order to extract the first 3,000 genes. Only deviations equal or above 0.585 (1.5 fold change) and equal or below -0.585 (-1.5 fold change) were considered as significant.Supervised learning: Significance Analysis of microarrays (SAM, []). SAM analyses were performed using Flexarray software using the normalized data of the 45,000 probesets. Data with p-values equal or below 0.01 and False Discover Rates (Benjamini Hochberg) equal or below 0.20 were included in further analyses. The data were ranked in decreasing order of the SAM d-score to obtain the list of the differentially expressed genes.The NetAffx website (Affymetrix, Santa Clara, CA, USA) was used to retrieve gene ontology (GO) annotations, probe sequences, and was utilized as a link to Unigene (NCBI) for further functional studies.The microarray dataset was deposited at Gene Expression Omnibus under accession number [GSE12581]. […]

Pipeline specifications

Software tools GeneCluster, SAM
Application Gene expression microarray analysis
Organisms Mus musculus, Homo sapiens
Diseases Leukemia