arrow plot a new graphical tool for selecting up and down regulated genes and genes differentially expressed on sample subgroups箭头画一个新的图形工具选择上下调节基因和基因差异表达样本子组.pdfVIP

Silva-Fortes et al. BMC Bioinformatics 2012, 13:147 /1471-2105/13/147 METHODOLOGY ARTICLE Open Access Arrow plot: a new graphical tool for selecting up and down regulated genes and genes differentially expressed on sample subgroups 1* ´ 2 2 Carina Silva-Fortes , Maria Antonia Amaral Turkman and Lisete Sousa Abstract Background: A common task in analyzing microarray data is to determine which genes are differentially expressed across two (or more) kind of tissue samples or samples submitted under experimental conditions. Several statistical methods have been proposed to accomplish this goal, generally based on measures of distance between classes. It is well known that biological samples are heterogeneous because of factors such as molecular subtypes or genetic background that are often unknown to the experimenter. For instance, in experiments which involve molecular classification of tumors it is important to identify significant subtypes of cancer. Bimodal or multimodal distributions often reflect the presence of subsamples mixtures. Consequently, there can be genes differentially expressed on sample subgroups which are missed if usual statistical approaches are used. In this paper we propose a new graphical tool which not only identifies genes with up and down regulations, but also genes with differential expression in different subclasses, that are usually missed if current statistical methods are used. This tool is based on two measures of distance between samples, namely the overlapping coefficient (OVL) between two densities and the area under the receiver operating characteristic (ROC) curve. The methodology proposed here was implemented in the open-source R software. Results: This method was applied to a pub