Comput Biol Chem - Meta-analysis of microarray data: The case of imatinib resistance in chronic myelogenous leukemia.

Tópicos

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Resumo

With the proliferation of related microarray studies by independent groups, a natural approach to analysis would be to combine the results across studies. In this article, we address a meta-analysis of the gene expression data on imatinib resistance in chronic myelogenous leukemia. First, an analysis of the overlapping among 6 published studies revealed that only 3 genes were coincident between 2 studies. A later reprocessing using different methods on 4 publicly available datasets revealed that 2 extra genes were overlapped between two sets. Both poor overlappings may be due to large differences in the sample source, the microarray platforms used, and a small difference in gene expression between the imatinib non-responder and responder patients. A search of common genes inside 4 public datasets afforded 404 well defined genes. Nevertheless, this necessary condition for meta-analysis caused the loss of many genes of possible interest. The expression signals of the common genes in the four datasets were reanalyzed using three summary statistical methods for combining quantitative information: Fisher, Stouffer and effect-size. Taking the three methods together and using an FDR<0.10 threshold, a gene-list with 33 differentially expressed genes was found. Considering all the reanalysis approaches used in this work, a final gene-list with 38 differentially expressed genes is reported. Despite the important limitations to this microarray meta-analysis, the presented procedures and integrated gene-list may have some potential value as regards imatinib resistance in CML patients since it is the first attempt to integrate evidence about gene-lists in this area.

Resumo Limpo

prolifer relat microarray studi independ group natur approach analysi combin result across studi articl address metaanalysi gene express data imatinib resist chronic myelogen leukemia first analysi overlap among publish studi reveal gene coincid studi later reprocess use differ method public avail dataset reveal extra gene overlap two set poor overlap may due larg differ sampl sourc microarray platform use small differ gene express imatinib nonrespond respond patient search common gene insid public dataset afford well defin gene nevertheless necessari condit metaanalysi caus loss mani gene possibl interest express signal common gene four dataset reanalyz use three summari statist method combin quantit inform fisher stouffer effects take three method togeth use fdr threshold genelist differenti express gene found consid reanalysi approach use work final genelist differenti express gene report despit import limit microarray metaanalysi present procedur integr genelist may potenti valu regard imatinib resist cml patient sinc first attempt integr evid genelist area

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