Figure 1: | Scientific Reports

Figure 1

From: Quantifying the relative immune cell activation from whole tissue/organ-derived differentially expressed gene data

Figure 1

Sample and data processing scheme in ICEPOP analysis. (a) Sample processing scheme of quantifying immune cell activation from tissue- or organ-derived differential expression genes (DEGs). RNA is purified from a whole organ (e.g. spleen) or PBMC, and then gene expression is measured by microarray. Typical analysis requires control and treated sample pairs, and then their DEGs are used to determine the immune cell activation. (b) Data processing framework of ICEPOP analysis. First, species need to be specified. For sample derived from mouse liver, spleen, or lymph node, CV filter is available. For ICEPOP analysis, the user needs to set the fold-change threshold to select the actual input DEGs. ICEPOP calculates the relative activation score for each cell type using a scoring matrix, and then produces a bar graph and circular plot as outputs. Roman numerals (I, II, III) refer to the processes described in Supplementary Figure S2.