| Transcription factor binding: Does order matter? | |||||||||
| Gabriel Kreiman1 and Nambi Nallasamy1,2 | |||||||||
| 1Computation and Systems Biology Initiative, Massachusetts Institute of Technology | |||||||||
| 2Division of Engineering and Applied Sciences, Harvard University | |||||||||
| Supplementary Material | |||||||||
| Supplementary Figure 1 | |||||||||
| Supplementary Figure 2 | |||||||||
| Supplementary Figure 3 | |||||||||
| Supplementary Figure 4 | |||||||||
| Supplementary Figure 5 | |||||||||
| Supplementary Figure 6 | |||||||||
| Supplementary Table 1: List of PWMs used in this study | |||||||||
| A List of TFs used from yeast (Pilpel et al., 2001) | |||||||||
| B List of TFs used for humans and mouse (TRANSFAC release 6.0, public version | List of Gene IDs | ||||||||
| Supplementary Table 2: Putative binding sites statistics | |||||||||
| species | threshold | repeatmask | conserved | link | |||||
| hs | low FP | yes | no | link | |||||
| hs | low FN | yes | no | link | |||||
| hs | low FP | yes | yes | link | |||||
| hs | low FN | yes | yes | link | |||||
| mm | low FP | yes | no | link | |||||
| mm | low FN | yes | no | link | |||||
| mm | low FP | yes | yes | link | |||||
| mm | low FN | yes | yes | link | |||||
| sc | low FP | yes | no | link | |||||
| sc | low FN | yes | no | link | |||||
| Supplementary Table 3: Parameter landscape | |||||||||
| Number of significant pairs results for different parameters | |||||||||
| Supplementary Table 4: Summary of results | |||||||||
| threshold | repeatmask | conserved | link | ||||||
| low FP | yes | no | link | ||||||
| low FN | yes | no | link | ||||||
| low FP | yes | yes | link | ||||||
| low FN | yes | yes | link | ||||||
| Supplementary Table 5: Potential interactions | |||||||||
| Interactions for TF pairs from Table 1 | |||||||||
| threshold | repeatmask | conserved | link | ||||||
| low FP | yes | no | link | ||||||
| low FN | yes | no | link | ||||||
| low FP | yes | yes | link | ||||||
| low FN | yes | yes | link | ||||||
| Co-citations for all TF pairs, Google Scholar | |||||||||
| Co-citations for all TF pairs, PubMed | |||||||||
| All TF pairs present in MPPI | |||||||||
| All TF pairs present in HPREF | |||||||||
| All TF pairs present in Rual et al 2005 | |||||||||