Additional file 8 of Single-cell RNA sequencing of the retina in a model of retinitis pigmentosa reveals early responses to degeneration in rods and cones

Additional file 8. In silico position weight matrix analysis on transcripts differentially expressed in early degeneration. To determine which transcription factors might be associated with significantly differentially expressed transcripts identified in the early differential gene expression analysis (Additional file 2), we used Enrichr to perform an in silico search for sequence motifs representing transcription factor binding sites in the promoter region (-2000 to + 500 bp of the transcriptional start site) of these genes. The Overlap column refers to the number of genes in the input list (differentially regulated genes; numerator) compared to all genes in the database (denominator) that contain the transcription factor binding motif. P-values were calculated with Fisher’s exact test, and adjusted with the Benjamini-Hochberg method. The Combined Score is log(p-value)*z-score, where z-score is the deviation from the expected rank calculated from many random gene lists [57, 112].