Additional data file 1:

Table S1 includes a list of binding site motifs for known SFs used for training and testing the method. Table S2 summarizes the training results using different estimators and thresholds. Table S3 lists the thresholds used for the COS(WR) function for each binding site motif. Tables S4 and Table S5 display detailed results for the enrichment tests performed for AAs, CEs, and ADs, applying the COS(WR) and single score (S), respectively. Table S6 displays the values of the TSI calculated for the different SFs. Table S7 presents the details of the predicted SF-SF interactions. Table S8 displays the values for the background model calculated for the Single Scores (S).

Format: PDF Size: 322KB Download file

This file can be viewed with: Adobe Acrobat Reader

Additional data file 2:

Figure S1 illustrates the TPR of different multiplicity estimators (WR, WA, M, SS and S) calculated at a fixed false positive rate of 0.01. TPRs were calculated with and without the COS. Figure S2 demonstrates the analysis of the SF2/ASF and NOVA-1 CLIP datasets, when applying (a, c) COS(WR) and (b, d) Single Scores. Figure S3 is a heat map representing the calculated enrichment of SFBSs around different alternative events, when applying Single Scores (S) only.

Format: PDF Size: 7.6MB Download file

This file can be viewed with: Adobe Acrobat Reader

Additional data file 3:

Experimentally defined SFBSs used for training and testing.

Format: TXT Size: 53KB Download file

Additional data file 4:

SFF standalone download, suitable for running under the Linux OS.

Format: ZIP Size: 6KB Download file