Transcriptional regulatory network of developing mouse telencephalon

In mouse, a vesicle forms at the anterior part of the developing embryo at 9.5 day/stage (M9.5), which further develops into telencephalon at M10.5 day/stage. The equivalent stages in chick embryo are referred to as HH17 and HH24. We sequenced RNA populations from telencephalic region at the early (M9.5 and HH17) and late stages (M10.5 and HH24) of mouse and chick embryo. Four samples were sequenced for each stage of telencephalon development. The resulting RNA sequencing reads were used to assemble transcripts and for counting their abundance. The read counts for each transcript then used to compute its differential expression between M9.5 and M10.5 stages in mouse. Likewise, each chick transcript was compared between H17 and HH24 stages. Genes having significant p-values with positive log2 -fold change represent increased expression at developmental stage B (late) compared to stage A (early) and are referred to as up-regulated (UP). Likewise, genes with negative log2-fold change represent decreased expression at stage B compared to stage A and are referred to as down-regulated (Down, DN). Gene expression with p-values above 0.05 was considered non-significant and represents no change between stage B and stage A and is referred to as no change (NC). Genes with read count roughly less than five in less than four samples were considered not expressed and referred to as NE. These four groups of genes were further categorized into sixteen groups based on the expression status of mouse and chick gene orthologs. These sixteen gene groups; UP, DN, NC, and NE mouse gene groups; and a gene group composed of all differentially expressed genes in mouse (DEG), were submitted to iRegulon Cytoscape plugin for predicting their transcriptional regulatory factors. These gene groups and iRegulon prediction results for each of the groups are provided as datasets. Using significant iRegulon prediction results, we reconstructed transcriptional regulatory network for mouse telencephalon development, which is also provided as network file. In addition to a single excel file containing results for some of the gene groups where we found meaningful connection between the predicted transcription factors and their differentially expressed targets genes.