There are 4 folders under this directory. (1) Software Inside this folder, there are two versions of SIOMICS software. (Windows and Linux). (2) inputseq Inside this folder, there are extended 13 ChIP-seq peaks in 13 mESC. Our predictions in this paper were using those 13 datasets. (3) SIOMICS_Prediction_Results Inside this folder, there are SIOMICS prediction results on 13 mESC TF ChIP-seq peaks. Please note: The comparison results : X.motifs.JASPAR.pdf and X.motifs.TRANSFAC.pdf are only containing best 5 matches for each predicted motif to the known motif databases(JASPAR and TRANSFAC). If we put all matches smaller than given E-value threshold (say,E-4), X.motifs.JASPAR.pdf and X.motifs.TRANSFAC.pdf will be too large(hundreds of pages pdf) to be read, thus we only kept the top 5 matches in those two files. A few co-factors mentioned in the paper may be missing here, but you can always find them from the corresponding results in folder "Comparison_SIOMICS_Predictions_with_Known_Motifs_In_JASPAR_TRANSFAC". (4) Comparison_SIOMICS_Predictions_with_Known_Motifs_In_JASPAR_TRANSFAC Inside this folder, we provide an compact and integrated comparison results between predicted motifs and known motif databases. In this result, the comparisons between JASPAR and TRANSFAC will be combined and shown in a text file. Besides, top 10 matches for each predicted motifs were provided and therefore the comparison is much more complete.