Interpretation of Taiji result for transcriptional repressors

[YM-Chuang]

Dear Taiji authors,

Thanks for establishing this powerful tool for key TF network analysis.

We have done the Taiji analysis for integrating ATAC-seq and RNA-seq recently, and we are confused about the interpretation of transcription factors which play the role for suppress target gene expression.

Based on the Taiji framework, it seems the active chromatin region will be taken into consideration, and the transcriptomic information will be also considered in the following. But we are curious that how the algorithm processes the gene which has active chromatin but lower expression in the sample. And also if the transcriptional factors belong to the repressor, should we convert the score we got into negative?

Thanks for your help and suggestions.