Fig. 1

Correlation matrix and MA-plot from ChRO-seq analysis. a Spearman’s rank correlation of 17 HSA (orange bar) and 4 Normal samples (green bar). The sample order is based on single-linked hierarchical clustering of the matrix, shown by the dendrogram. 7007 genes (> 20 rpkm) were used to calculate the correlation coefficients by GENE-E. b MA-plot of DESeq2 analysis. Results show that ECM-associated gene expression tends to be upregulated in HSA while genes involved in normal splenic function tend to be downregulated. X-axis represents average expression over all samples. Y-axis represents log2 fold change between HSA and normal. Genes with an adjusted p-value below 0.01 are shown in red. c Heatmap of differentially expressed genes with hierarchical clustering of samples. Differentially expressed genes from DEseq analysis (FDR < 0.001) were examined to evaluate gene expression levels in individual samples