Influence factors on the correlations between expression levels of neighboring pattern genes

•The correlation between expression levels (CEL) of neighboring non-pattern genes is related to multiple factors with the exception of transcriptional orientations of neighboring genes.•The CEL of neighboring Spgenes or Regenes is likely to be dependent on the co-functions of neighboring genes.•The CEL of neighboring HKgenes is associated with modification levels in intergenic regions.

Some genes tend to cluster and be co-expressed. Multiple factors affect gene co-expression. In this study, we investigated the relationships between multiple factors and the correlations of expression levels of neighboring genes, which were divided into four kinds of pattern genes and one type of non-pattern gene. Our results indicate that the correlation between expression levels of neighboring non-pattern genes is related to multiple factors with the exception of transcriptional orientations of neighboring genes. The correlation between expression levels of neighboring specific genes or neighboring repressed genes is likely to be dependent on the co-functions of neighboring genes. The correlation between expression levels of neighboring housekeeping genes is associated with histone modifications in intergenic regions.