A SELF-ATTENTION MODEL FOR INFERRING REGULATORY INTERACTIONS

Supplementary Methods

Data collection and processing

A. Experiment 1: Simulated dataset In this experiment, we simulated DNA sequences using random sampling from a distribution of [0.27, 0.23, 0.23, 0.27] for A, C, G, and T respectively as used for a similar dataset generated by Greenside et al. [1]. We generated 120,000 sequences each with a length of 200 bp. Similar to Greenside et al. [1], we randomly embedded instances of the motifs of both ELF1 and SIX5 transcription factors in 40,000 of the total sequences. This was our positive set of examples where we essentially simulated interactions between the aforementioned motifs. In the negative set (80,000 sequences), we embedded instances of either ELF1 or SIX5 in a sequence (but not both). Moreover, we embedded instances of the AP1 and TAL1 motifs across all examples. The motifs for the four transcription factors were obtained from Kheradpour et al. [2].

TF Database information To map CNN filters to motifs of known TFs, we used TomTom with a custom TF database (MEME format) containing PWMs of the four transcription factors: SIX5, ELF1, AP1, and TAL1.

B. Experiment 2: TAL-GATA ChIP-peaks Here we followed the same strategy described in DFIM [1]: ChIP-Seq peaks were downloaded for the three TFs TAL1, GATA1, and GATA2 from the ENCODE [4] database in the K562 cell line (hg19 genome assembly and annotations). For the chromatin accessibility data, we downloaded processed DNase I Hypersensitive Sites (DHSs) from the ENCODE database for the corresponding cell line. Next, every ChIP-Seq peak for the three transcription factors was searched for an overlap with DHSs in the K562 cell line. If an overlap was found, the sequence of the ChIP-Seq peak was extended 500 bp upstream and downstream from its center. This served as a positive set in our binary classification problem. For the negative set, we randomly sampled 80,000 examples from all K562 DHSs that didn’t overlap a ChIP-Seq peak for any of the three transcription factors.

TF Database information In this experiment, we used two TF databases: the first one was a custom motif file with PWMs of TAL1, GATA1, and GATA2 transcription factors. This was because we wanted to directly compare our model to DFIM [1] where Greenside et al. measured interactions between the aforementioned transcription factors. The second reference was the entire CISBP TF database [3] that we used in order to infer other TF interactions within the ChIP-Seq peaks.

C. Experiment 3: Human promoter DHSs In this experiment, we used DHSs overlapping gene promoter regions across the entire human genome. We used the pipeline described by Kelley et al. in Basset [5]: DHSs were downloaded for 164 human immortalized cell lines from the ENCODE [4] and ROADMAP [6] consortia. These regions of open chromatin were merged if they overlapped more than 200 bp. Finally, A SELF-ATTENTION MODEL FOR INFERRING REGULATORY INTERACTIONS

every DHS was extended to a length of 600 bp around its center. Kelley et al. [5] used DHSs across the entire genome however, we selected only those which overlapped the human promoter regions. To do that, we defined promoter as a region of 1000 bp upstream of the transcription start site (TSS) of a gene—Ensemble based hg19/GrCh37 reference and annotations were used. The final dataset had 20,613 genomic sequences of the corresponding DHSs (that overlapped the human promoters). The targets in this case were either a single or multiple labels, corresponding to the164 cell lines in which the DHSs were observed.

TF Database information In motif analysis (and later in the TF interactions), we used the human CISBP transcription factor database [3].

D. Experiment 4: Genome-wide arabidopsis regions of open chromatin Here we designed a similar experiment as described in the previous section. The dataset was constructed using the same procedure described above as used by Kelley et al. [5]. We used regions of open chromatin: DHSs and ATAC-Seq based Transposase Hypersensitive Sites (THSs), across the entire arabidopsis genome using TAIR10 annotations. We used the following publicly available datasets (GEO accession numbers provided):

1. For DHSs: GSE53322, GSE53324, GSE53323, GSE46987, GSE34318 2. For THSs: GSE89346, GSE85203, GSE101940, GSE116287, GSE101482

We ended up with 88,245 examples in our final dataset across 36 different samples. Note that peaks occurring in multiple biological samples were merged.

TF Database information Here we used the DAP-Seq based arabidopsis transcription factors database [7].

Limitations of the TomTom motif comparison tool We used the TomTom tool from the MEME suite [8] to map CNN filters to motifs of known transcription factors. In some cases, we observed the match to be dubious despite the tool assigning it a significant p-value. This is shown in Supplementary Figure F4 for two of our CNN filters matching the known TF motifs of HOXA2 and ZNF263 in the human CISBP database [3]. By default, TomTom uses Pearson correlation for comparing motifs. However, we obtained better results using the Euclidean distance.

A SELF-ATTENTION MODEL FOR INFERRING REGULATORY INTERACTIONS

Supplementary Figures

Figure F1: Distribution of the attention values for the test and the background sets. The actual frequencies (y-axis) are normalized by total sizes of the test and background sets. This figure helps in selecting the appropriate attention cutoff, one of the parameters of SATORI. We use a default value of 0.10.

Figure F2: Similarities between motifs of GATA variants (a). Similarly, TAL1 and TCF15, both belonging to the bHLH family, have very similar motifs (CAGCTG consensus) (b).

A SELF-ATTENTION MODEL FOR INFERRING REGULATORY INTERACTIONS

0.95

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0.85 MHA (AUC scores) MHA - 0.83 RNN - 0.81 CNN

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0.75 0.75 0.77 0.79 0.81 0.83 0.85 0.87 0.89 0.91 0.93 0.95 CNN-MHA (AUC scores)

Figure F3: AUC scores for DHSs in human promoters across 164 cell types, achieved by the two model variants. Each circle represents performance on detecting DHSs in that cell line.

Figure F4: Limitations of the TomTom motif comparison tool. Matches shown here are detected as statistically significant (q-value < 0.01) for both (a) HOXA2 and (b) ZNF263. The top row depicts the gold standard motif in the CISBP database and the bottom row shows the CNN filter/motif.

A SELF-ATTENTION MODEL FOR INFERRING REGULATORY INTERACTIONS

Figure F5: The most frequent interacting transcription factor families in human promoter regions.

A SELF-ATTENTION MODEL FOR INFERRING REGULATORY INTERACTIONS

Supplementary Tables

Table S1: List of neural network hyperparameters.

Hyperparameter type Description singlehead_size int Size of the attention head [default: 32] num_heads int Number of heads in multi-head self-attention layer [default: 8] multihead_size int Output size of the multi-head after concatenation [default: 100] batch_size int Batch size in training/testing the model [default: 172] use_RNN bool Choose whether to use the RNN layer. [default: based on model variant] RNN_hidden_size int Size of the RNN layer. [default: 100] CNN_filters int Number of CNN filters to use. [default: 200] CNN_filter_size int Size of each CNN filter. [default: 13] use_CNN_pool bool Use max pooling in the CNN layer. [default: True] CNN_pool_size int Size of the max pooling window in CNN layer. [default: 6] input_channels int Number of input channels. [default: 4 (for DNA sequences)] num_epochs int Number of training epochs. [default: 30] readout_strategy string Whether to normalize the MHA output or flatten it. [default: "normalize"]

Table S2: Summary of all significant interactions in the simulated/toy dataset. Our model is able to recover multiple interactions involving SIX5 and ELF1 TF motifs. We also provide the actual CNN filter interactions in the first column, named based on the total number of filters in the convolutional layer.

Filter interaction TF motif interaction Adjusted p-value filter033⟷filter170 SIX5⟷ELF1 1.47E-42 filter170⟷filter181 ELF1⟷SIX5 1.50E-39 filter033⟷filter111 SIX5⟷ELF1 1.12E-20 filter111⟷filter181 ELF1⟷SIX5 3.17E-22 filter033⟷filter091 SIX5⟷ELF1 2.44E-18 filter091⟷filter181 ELF1⟷SIX5 2.14E-12 filter033⟷filter055 SIX5⟷ELF1 2.64E-08 filter055⟷filter181 ELF1⟷SIX5 3.84E-04 filter019⟷filter033 ELF1⟷SIX5 1.35E-07 filter019⟷filter181 ELF1⟷SIX5 2.48E-12 filter091⟷filter199 ELF1⟷SIX5 2.82E-03

A SELF-ATTENTION MODEL FOR INFERRING REGULATORY INTERACTIONS

Table S3: All significant interactions between TAL1 and GATA transcription factors. Note that in this case, a custom TF database was used containing motifs for TAL1, GATA1, and GATA2. In case of TAL1, other TFs (LYL1, NHLH2, and TAL2) also shared the same binding site motif and hence are mentioned here.

TF A TF B Adjusted p-value GATA2 LYL1,TAL1,NHLH2,TAL2 4.37E-24 GATA2 LYL1,TAL1,NHLH2,TAL2 8.18E-21 LYL1,TAL1,NHLH2,TAL2 GATA2 5.71E-19 LYL1,TAL1,NHLH2,TAL2 GATA2 1.54E-16 LYL1,TAL1,NHLH2,TAL2 GATA2 8.68E-11 GATA2 LYL1,TAL1,NHLH2,TAL2 3.92E-10 LYL1,TAL1,NHLH2,TAL2 GATA2 3.27E-08 LYL1,TAL1,NHLH2,TAL2 GATA2 3.28E-08 GATA2 LYL1,TAL1,NHLH2,TAL2 5.66E-05 LYL1,TAL1,NHLH2,TAL2 GATA2 6.76E-04 LYL1,TAL1,NHLH2,TAL2 GATA2 4.51E-03 LYL1,TAL1,NHLH2,TAL2 GATA2 4.66E-03 LYL1,TAL1,NHLH2,TAL2 GATA2 4.72E-03 LYL1, TAL1,NHLH2,TAL2 GATA2 5.41E-03

Table S6: A list of known TF interactions identified by our model in the human promoter dataset. TRRUSTv2 [9] was used as a reference for known interactions. The level of significance (adjusted p-value) assigned by our model to each interaction is provided in the last column.

motif interaction TF1 family TF2 family adjusted p-value EGR1⟷LCOR C2H2 ZF Pipsqueak 1.84E-27 E2F1⟷LCOR E2F Pipsqueak 1.32E-23 DNMT1⟷LCOR CxxC Pipsqueak 1.72E-16 EGR1⟷SRF C2H2 ZF MADS box 1.75E-14 SRF⟷SP2 MADS box C2H2 ZF 4.12E-10 E2F1⟷SRF E2F MADS box 5.96E-09 EGR1⟷E2F4 C2H2 ZF E2F 9.64E-07 E2F1⟷DNMT1 E2F CxxC 4.36E-05 E2F1⟷E2F4 E2F E2F 1.64E-04 DNMT1⟷E2F4 CxxC E2F 1.64E-04 E2F1⟷EGR1 E2F C2H2 ZF 1.99E-03 DNMT1⟷EGR1 CxxC C2H2 ZF 2.33E-03

A SELF-ATTENTION MODEL FOR INFERRING REGULATORY INTERACTIONS

Table S7: Summary of the number of unique statistically significant TF interactions reported by SATORI and FIS for the three real-world datasets.

Experiment SATORI FIS TAL-GATA ChIP-Seq 152 235 Human promoters 234 184 Arabidopsis genome-wide 230 224

Table S4: A list of all unique TF interactions in the TAL-GATA ChIP-Seq peaks dataset. (appended to this supplement.)

Table S5: A list of all unique significant interactions in the human promoters. (appended to this supplement.)

References 1. Greenside, P., Shimko, T., Fordyce, P., & Kundaje, A. (2018). Discovering epistatic feature interactions from neural network models of regulatory DNA sequences. Bioinformatics, 34(17), i629-i637. 2. Kheradpour, P., & Kellis, M. (2014). Systematic discovery and characterization of regulatory motifs in ENCODE TF binding experiments. Nucleic acids research, 42(5), 2976-2987. 3. Lambert, S. A., Jolma, A., Campitelli, L. F., Das, P. K., Yin, Y., Albu, M., ... & Weirauch, M. T. (2018). The human transcription factors. Cell, 172(4), 650-665. 4. Gerstein, M. B., Kundaje, A., Hariharan, M., Landt, S. G., Yan, K. K., Cheng, C., ... & Min, R. (2012). Architecture of the human regulatory network derived from ENCODE data. Nature, 489(7414), 91-100. 5. Kelley, D. R., Snoek, J., & Rinn, J. L. (2016). Basset: learning the regulatory code of the accessible genome with deep convolutional neural networks. Genome research, 26(7), 990-999. 6. Kundaje, A., Meuleman, W., Ernst, J., Bilenky, M., Yen, A., Heravi-Moussavi, A., ... & Amin, V. (2015). Integrative analysis of 111 reference human epigenomes. Nature, 518(7539), 317-330. 7. Bartlett, A., O'Malley, R. C., Huang, S. S. C., Galli, M., Nery, J. R., Gallavotti, A., & Ecker, J. R. (2017). Mapping genome-wide transcription-factor binding sites using DAP-seq. Nature protocols, 12(8), 1659. 8. Bailey, T. L., Johnson, J., Grant, C. E., & Noble, W. S. (2015). The MEME suite. Nucleic acids research, 43(W1), W39-W49. 9. Han, H., Cho, J. W., Lee, S., Yun, A., Kim, H., Bae, D., ... & Lee, S. (2018). TRRUST v2: an expanded reference database of human and mouse transcriptional regulatory interactions. Nucleic acids research, 46(D1), D380-D386.

Table S4: TAL-GATA unique TF interactions filter_interaction TF_interaction Family_Interaction adjusted_pval filter9⟷filter65 GATA4⟷ZKSCAN1 C2H2 ZF⟷GATA 4.37E-37 filter9⟷filter114 GATA4⟷TLX2 Homeodomain⟷GATA 2.04E-35 filter65⟷filter114 ZKSCAN1⟷TLX2 Homeodomain⟷C2H2 ZF 4.96E-35 filter65⟷filter73 KDM2B⟷ZKSCAN1 C2H2 ZF⟷CxxC 1.61E-31 filter73⟷filter114 KDM2B⟷TLX2 Homeodomain⟷CxxC 1.91E-30 filter9⟷filter127 GATA4⟷KDM2B GATA⟷CxxC 2.62E-30 filter9⟷filter136 GATA4⟷GATA5 GATA⟷GATA 2.70E-23 filter65⟷filter161 ZNF35⟷ZKSCAN1 C2H2 ZF⟷C2H2 ZF 1.33E-22 filter114⟷filter136 GATA5⟷TLX2 Homeodomain⟷GATA 2.87E-22 filter9⟷filter169 GATA4⟷TCF15 GATA⟷bHLH 1.71E-21 filter9⟷filter161 GATA4⟷ZNF35 C2H2 ZF⟷GATA 2.67E-21 filter9⟷filter13 ZNF202⟷GATA4 C2H2 ZF⟷GATA 8.92E-21 filter9⟷filter194 GATA4⟷HOXA2 Homeodomain⟷GATA 1.10E-19 filter9⟷filter47 GATA4⟷DMRTA2 GATA⟷DM 7.50E-19 filter73⟷filter136 KDM2B⟷GATA5 GATA⟷CxxC 1.98E-18 filter8⟷filter114 AIRE⟷TLX2 SAND⟷Homeodomain 2.62E-18 filter114⟷filter161 ZNF35⟷TLX2 Homeodomain⟷C2H2 ZF 5.01E-18 filter65⟷filter136 ZKSCAN1⟷GATA5 C2H2 ZF⟷GATA 8.61E-18 filter65⟷filter80 ZKSCAN1⟷GATA2 C2H2 ZF⟷GATA 1.25E-17 filter8⟷filter9 AIRE⟷GATA4 SAND⟷GATA 1.31E-17 filter8⟷filter65 AIRE⟷ZKSCAN1 SAND⟷C2H2 ZF 1.85E-17 filter114⟷filter145 TCF15⟷TLX2 Homeodomain⟷bHLH 4.19E-17 filter65⟷filter169 ZKSCAN1⟷TCF15 C2H2 ZF⟷bHLH 7.17E-17 filter114⟷filter194 HOXA2⟷TLX2 Homeodomain⟷Homeodomain 1.69E-16 filter9⟷filter56 GATA4⟷ESR1 GATA⟷Nuclear receptor 2.50E-16 filter80⟷filter114 TLX2⟷GATA2 Homeodomain⟷GATA 4.22E-16 filter59⟷filter65 ZNF202⟷ZKSCAN1 C2H2 ZF⟷C2H2 ZF 4.54E-16 filter37⟷filter65 SOX1⟷ZKSCAN1 C2H2 ZF⟷Sox 6.01E-16 filter9⟷filter46 GATA4⟷RARG GATA⟷Nuclear receptor 6.83E-16 filter9⟷filter131 GATA4⟷PRKRIR GATA⟷THAP finger 8.20E-16 filter9⟷filter37 GATA4⟷SOX1 GATA⟷Sox 1.12E-15 filter80⟷filter127 KDM2B⟷GATA2 GATA⟷CxxC 1.15E-15 filter9⟷filter80 GATA4⟷GATA2 GATA⟷GATA 1.18E-15 filter65⟷filter131 ZKSCAN1⟷PRKRIR C2H2 ZF⟷THAP finger 1.25E-14 filter65⟷filter194 HOXA2⟷ZKSCAN1 Homeodomain⟷C2H2 ZF 1.66E-14 filter37⟷filter114 SOX1⟷TLX2 Homeodomain⟷Sox 3.01E-14 filter9⟷filter67 GATA4⟷HOXA11 Homeodomain⟷GATA 4.98E-14 filter13⟷filter114 ZNF202⟷TLX2 Homeodomain⟷C2H2 ZF 1.48E-13 filter47⟷filter65 DMRTA2⟷ZKSCAN1 DM⟷C2H2 ZF 2.52E-13 filter47⟷filter114 DMRTA2⟷TLX2 Homeodomain⟷DM 5.66E-13 filter73⟷filter148 KDM2B⟷ZNF35 C2H2 ZF⟷CxxC 8.52E-13 filter9⟷filter123 GATA4⟷DNMT1 GATA⟷CxxC 3.95E-12 filter127⟷filter145 KDM2B⟷TCF15 CxxC⟷bHLH 1.01E-11 filter56⟷filter65 ESR1⟷ZKSCAN1 Nuclear receptor⟷C2H2 ZF 1.43E-11 filter65⟷filter67 ZKSCAN1⟷HOXA11 Homeodomain⟷C2H2 ZF 1.69E-11 filter114⟷filter131 TLX2⟷PRKRIR Homeodomain⟷THAP finger 3.11E-11 filter9⟷filter63 GATA4⟷IRX4 Homeodomain⟷GATA 4.91E-11 filter127⟷filter194 HOXA2⟷KDM2B Homeodomain⟷CxxC 1.54E-10 filter64⟷filter123 ZKSCAN1⟷DNMT1 C2H2 ZF⟷CxxC 1.92E-10 filter80⟷filter145 TCF15⟷GATA2 GATA⟷bHLH 2.08E-10 filter9⟷filter167 GATA4⟷SP7 C2H2 ZF⟷GATA 2.50E-10 filter67⟷filter114 HOXA11⟷TLX2 Homeodomain⟷Homeodomain 3.33E-10 filter59⟷filter73 ZNF202⟷KDM2B C2H2 ZF⟷CxxC 4.38E-10 filter145⟷filter161 ZNF35⟷TCF15 C2H2 ZF⟷bHLH 5.93E-10 filter56⟷filter114 ESR1⟷TLX2 Homeodomain⟷Nuclear receptor 7.57E-10 filter13⟷filter80 ZNF202⟷GATA2 C2H2 ZF⟷GATA 1.15E-09 filter59⟷filter136 ZNF202⟷GATA5 C2H2 ZF⟷GATA 1.31E-09 filter80⟷filter136 GATA5⟷GATA2 GATA⟷GATA 1.44E-09 filter56⟷filter80 ESR1⟷GATA2 GATA⟷Nuclear receptor 1.49E-09 filter47⟷filter127 KDM2B⟷DMRTA2 CxxC⟷DM 5.10E-09 filter8⟷filter73 AIRE⟷KDM2B SAND⟷CxxC 5.65E-09 filter65⟷filter167 ZKSCAN1⟷SP7 C2H2 ZF⟷C2H2 ZF 8.88E-09 filter136⟷filter145 GATA5⟷TCF15 GATA⟷bHLH 1.17E-08 filter46⟷filter65 RARG⟷ZKSCAN1 Nuclear receptor⟷C2H2 ZF 1.55E-08 filter37⟷filter127 KDM2B⟷SOX1 CxxC⟷Sox 1.71E-08 filter63⟷filter65 IRX4⟷ZKSCAN1 Homeodomain⟷C2H2 ZF 2.48E-08 filter80⟷filter148 ZNF35⟷GATA2 C2H2 ZF⟷GATA 5.02E-08 filter73⟷filter138 KDM2B⟷PRKRIR CxxC⟷THAP finger 5.51E-08 filter46⟷filter114 RARG⟷TLX2 Homeodomain⟷Nuclear receptor 5.95E-08 filter8⟷filter80 AIRE⟷GATA2 SAND⟷GATA 1.26E-07 filter47⟷filter145 DMRTA2⟷TCF15 DM⟷bHLH 3.08E-07 filter136⟷filter148 ZNF35⟷GATA5 C2H2 ZF⟷GATA 3.60E-07 filter47⟷filter80 DMRTA2⟷GATA2 GATA⟷DM 3.68E-07 filter9⟷filter110 GATA4⟷MLL GATA⟷CxxC 4.78E-07 filter13⟷filter161 ZNF202⟷ZNF35 C2H2 ZF⟷C2H2 ZF 6.08E-07 filter8⟷filter145 AIRE⟷TCF15 SAND⟷bHLH 6.93E-07 filter2⟷filter9 HHEX⟷GATA4 Homeodomain⟷GATA 7.17E-07 filter67⟷filter127 HOXA11⟷KDM2B Homeodomain⟷CxxC 8.38E-07 filter59⟷filter138 ZNF202⟷PRKRIR C2H2 ZF⟷THAP finger 1.40E-06 filter56⟷filter127 ESR1⟷KDM2B CxxC⟷Nuclear receptor 1.62E-06 filter65⟷filter110 ZKSCAN1⟷MLL C2H2 ZF⟷CxxC 2.57E-06 filter9⟷filter44 GATA4⟷ENSG00000235187 GATA⟷Ets 3.08E-06 filter80⟷filter194 HOXA2⟷GATA2 Homeodomain⟷GATA 4.32E-06 filter80⟷filter123 GATA2⟷DNMT1 GATA⟷CxxC 5.31E-06 filter8⟷filter161 AIRE⟷ZNF35 SAND⟷C2H2 ZF 1.26E-05 filter114⟷filter123 TLX2⟷DNMT1 Homeodomain⟷CxxC 1.28E-05 filter18⟷filter161 HOXA2⟷ZNF35 Homeodomain⟷C2H2 ZF 1.35E-05 filter37⟷filter145 SOX1⟷TCF15 Sox⟷bHLH 1.46E-05 filter110⟷filter114 MLL⟷TLX2 Homeodomain⟷CxxC 1.76E-05 filter8⟷filter136 AIRE⟷GATA5 SAND⟷GATA 1.77E-05 filter123⟷filter127 KDM2B⟷DNMT1 CxxC⟷CxxC 2.24E-05 filter138⟷filter148 ZNF35⟷PRKRIR C2H2 ZF⟷THAP finger 2.66E-05 filter18⟷filter145 HOXA2⟷TCF15 Homeodomain⟷bHLH 2.76E-05 filter37⟷filter80 SOX1⟷GATA2 GATA⟷Sox 3.35E-05 filter18⟷filter59 ZNF202⟷HOXA2 Homeodomain⟷C2H2 ZF 4.46E-05 filter56⟷filter136 ESR1⟷GATA5 GATA⟷Nuclear receptor 5.28E-05 filter37⟷filter148 SOX1⟷ZNF35 C2H2 ZF⟷Sox 6.33E-05 filter46⟷filter73 KDM2B⟷RARG CxxC⟷Nuclear receptor 7.35E-05 filter59⟷filter145 ZNF202⟷TCF15 C2H2 ZF⟷bHLH 0.000105727 filter80⟷filter117 GATA2⟷PRKRIR GATA⟷THAP finger 0.000119018 filter13⟷filter37 ZNF202⟷SOX1 C2H2 ZF⟷Sox 0.000198947 filter8⟷filter37 AIRE⟷SOX1 SAND⟷Sox 0.000217494 filter37⟷filter136 SOX1⟷GATA5 GATA⟷Sox 0.000224019 filter136⟷filter138 PRKRIR⟷GATA5 GATA⟷THAP finger 0.000224053 filter44⟷filter65 ENSG00000235187⟷ZKSCAN1 Ets⟷C2H2 ZF 0.000226542 filter8⟷filter59 AIRE⟷ZNF202 SAND⟷C2H2 ZF 0.000228843 filter47⟷filter136 DMRTA2⟷GATA5 GATA⟷DM 0.000246003 filter114⟷filter167 TLX2⟷SP7 Homeodomain⟷C2H2 ZF 0.000273209 filter110⟷filter127 KDM2B⟷MLL CxxC⟷CxxC 0.000273836 filter47⟷filter161 DMRTA2⟷ZNF35 DM⟷C2H2 ZF 0.000385359 filter67⟷filter145 HOXA11⟷TCF15 Homeodomain⟷bHLH 0.000408805 filter2⟷filter114 HHEX⟷TLX2 Homeodomain⟷Homeodomain 0.000531496 filter8⟷filter47 AIRE⟷DMRTA2 SAND⟷DM 0.000629375 filter63⟷filter114 IRX4⟷TLX2 Homeodomain⟷Homeodomain 0.000634922 filter46⟷filter161 RARG⟷ZNF35 Nuclear receptor⟷C2H2 ZF 0.000668412 filter67⟷filter80 HOXA11⟷GATA2 Homeodomain⟷GATA 0.000753874 filter47⟷filter59 DMRTA2⟷ZNF202 DM⟷C2H2 ZF 0.000839157 filter46⟷filter80 RARG⟷GATA2 GATA⟷Nuclear receptor 0.00085175 filter18⟷filter37 HOXA2⟷SOX1 Homeodomain⟷Sox 0.000865659 filter123⟷filter161 DNMT1⟷ZNF35 C2H2 ZF⟷CxxC 0.000898244 filter59⟷filter123 ZNF202⟷DNMT1 C2H2 ZF⟷CxxC 0.001002915 filter18⟷filter136 HOXA2⟷GATA5 Homeodomain⟷GATA 0.001041611 filter46⟷filter59 RARG⟷ZNF202 Nuclear receptor⟷C2H2 ZF 0.001234011 filter127⟷filter167 KDM2B⟷SP7 C2H2 ZF⟷CxxC 0.001644866 filter63⟷filter127 IRX4⟷KDM2B Homeodomain⟷CxxC 0.002169677 filter104⟷filter138 SOX1⟷PRKRIR Sox⟷THAP finger 0.002217425 filter8⟷filter138 AIRE⟷PRKRIR SAND⟷THAP finger 0.002587796 filter59⟷filter67 ZNF202⟷HOXA11 Homeodomain⟷C2H2 ZF 0.002792003 filter18⟷filter138 HOXA2⟷PRKRIR Homeodomain⟷THAP finger 0.00298443 filter110⟷filter136 MLL⟷GATA5 GATA⟷CxxC 0.00334774 filter138⟷filter145 PRKRIR⟷TCF15 THAP finger⟷bHLH 0.003511075 filter56⟷filter138 ESR1⟷PRKRIR Nuclear receptor⟷THAP finger 0.003781693 filter8⟷filter46 AIRE⟷RARG SAND⟷Nuclear receptor 0.004836285 filter2⟷filter65 HHEX⟷ZKSCAN1 Homeodomain⟷C2H2 ZF 0.004952815 filter46⟷filter145 RARG⟷TCF15 Nuclear receptor⟷bHLH 0.005719193 filter44⟷filter127 ENSG00000235187⟷KDM2B Ets⟷CxxC 0.00623114 filter80⟷filter167 GATA2⟷SP7 C2H2 ZF⟷GATA 0.010195242 filter8⟷filter56 AIRE⟷ESR1 SAND⟷Nuclear receptor 0.010404602 filter18⟷filter56 HOXA2⟷ESR1 Homeodomain⟷Nuclear receptor 0.01300217 filter104⟷filter110 SOX1⟷MLL CxxC⟷Sox 0.013262636 filter56⟷filter161 ESR1⟷ZNF35 Nuclear receptor⟷C2H2 ZF 0.014167185 filter8⟷filter18 AIRE⟷HOXA2 SAND⟷Homeodomain 0.014444702 filter123⟷filter136 DNMT1⟷GATA5 GATA⟷CxxC 0.015830066 filter123⟷filter145 DNMT1⟷TCF15 CxxC⟷bHLH 0.018367261 filter67⟷filter161 HOXA11⟷ZNF35 Homeodomain⟷C2H2 ZF 0.021299458 filter37⟷filter47 SOX1⟷DMRTA2 Sox⟷DM 0.025453558 filter18⟷filter47 HOXA2⟷DMRTA2 Homeodomain⟷DM 0.026256523 filter67⟷filter136 HOXA11⟷GATA5 Homeodomain⟷GATA 0.029661419 filter47⟷filter138 DMRTA2⟷PRKRIR DM⟷THAP finger 0.031975285 filter56⟷filter126 ESR1⟷SOX1 Nuclear receptor⟷Sox 0.03802018 filter44⟷filter114 ENSG00000235187⟷TLX2 Ets⟷Homeodomain 0.039846485 filter110⟷filter145 MLL⟷TCF15 CxxC⟷bHLH 0.046305131 Table S5:Human promoters unique TF interactions filter_interaction TF_interaction Family_Interaction adjusted_pval filter37⟷filter178 EGR1⟷SP2 C2H2 ZF⟷C2H2 ZF 1.31E-71 filter178⟷filter193 SOX1⟷SP2 C2H2 ZF⟷Sox 6.96E-63 filter37⟷filter108 EGR1⟷ZNF263 C2H2 ZF⟷C2H2 ZF 3.61E-61 filter164⟷filter178 TLX2⟷SP2 C2H2 ZF⟷Homeodomain 3.28E-57 filter154⟷filter178 DMRTA2⟷SP2 C2H2 ZF⟷DM 1.60E-55 filter18⟷filter37 HOXA11⟷EGR1 C2H2 ZF⟷Homeodomain 7.98E-55 filter37⟷filter190 ZKSCAN1⟷EGR1 C2H2 ZF⟷C2H2 ZF 1.01E-54 filter108⟷filter178 ZNF263⟷SP2 C2H2 ZF⟷C2H2 ZF 6.79E-54 filter160⟷filter178 YBX2⟷SP2 C2H2 ZF⟷CSD 1.25E-52 filter37⟷filter69 EGR1⟷HHEX C2H2 ZF⟷Homeodomain 1.27E-51 filter37⟷filter164 TLX2⟷EGR1 C2H2 ZF⟷Homeodomain 1.41E-51 filter177⟷filter178 ZKSCAN1⟷SP2 C2H2 ZF⟷C2H2 ZF 1.88E-51 filter54⟷filter178 KDM2B⟷SP2 C2H2 ZF⟷CxxC 3.57E-51 filter133⟷filter178 E2F4⟷SP2 C2H2 ZF⟷E2F 6.13E-51 filter21⟷filter178 DNMT1⟷SP2 C2H2 ZF⟷CxxC 6.35E-51 filter37⟷filter193 EGR1⟷SOX1 C2H2 ZF⟷Sox 3.78E-50 filter37⟷filter41 KDM2B⟷EGR1 C2H2 ZF⟷CxxC 5.90E-50 filter37⟷filter133 EGR1⟷E2F4 C2H2 ZF⟷E2F 1.81E-49 filter4⟷filter37 E2F1⟷EGR1 C2H2 ZF⟷E2F 4.00E-49 filter37⟷filter160 EGR1⟷YBX2 C2H2 ZF⟷CSD 6.19E-49 filter18⟷filter178 HOXA11⟷SP2 C2H2 ZF⟷Homeodomain 8.74E-49 filter109⟷filter178 HHEX⟷SP2 C2H2 ZF⟷Homeodomain 1.01E-48 filter58⟷filter108 SOX1⟷ZNF263 C2H2 ZF⟷Sox 1.44E-48 filter6⟷filter178 SOX3⟷SP2 C2H2 ZF⟷Sox 1.49E-48 filter21⟷filter117 DNMT1⟷EGR1 C2H2 ZF⟷CxxC 1.79E-48 filter87⟷filter178 ZNF202⟷SP2 C2H2 ZF⟷C2H2 ZF 1.94E-48 filter149⟷filter178 MLL⟷SP2 C2H2 ZF⟷CxxC 2.42E-48 filter37⟷filter149 MLL⟷EGR1 C2H2 ZF⟷CxxC 1.27E-47 filter54⟷filter108 KDM2B⟷ZNF263 C2H2 ZF⟷CxxC 1.40E-47 filter4⟷filter178 E2F1⟷SP2 C2H2 ZF⟷E2F 2.37E-46 filter93⟷filter178 ZNF35⟷SP2 C2H2 ZF⟷C2H2 ZF 1.33E-45 filter108⟷filter192 TLX2⟷ZNF263 C2H2 ZF⟷Homeodomain 1.98E-45 filter71⟷filter108 ZKSCAN1⟷ZNF263 C2H2 ZF⟷C2H2 ZF 1.05E-44 filter157⟷filter178 LHX5⟷SP2 C2H2 ZF⟷Homeodomain 1.09E-44 filter37⟷filter114 EGR1⟷ZFY C2H2 ZF⟷C2H2 ZF 8.33E-44 filter169⟷filter178 SIX4⟷SP2 C2H2 ZF⟷Homeodomain 2.30E-42 filter108⟷filter169 ZNF263⟷SIX4 C2H2 ZF⟷Homeodomain 3.35E-42 filter4⟷filter108 E2F1⟷ZNF263 C2H2 ZF⟷E2F 3.92E-42 filter93⟷filter108 ZNF35⟷ZNF263 C2H2 ZF⟷C2H2 ZF 7.22E-42 filter4⟷filter18 E2F1⟷HOXA11 E2F⟷Homeodomain 1.05E-41 filter4⟷filter69 E2F1⟷HHEX E2F⟷Homeodomain 1.09E-41 filter153⟷filter178 LCOR⟷SP2 C2H2 ZF⟷Pipsqueak 1.28E-41 filter4⟷filter193 E2F1⟷SOX1 E2F⟷Sox 1.64E-41 filter108⟷filter133 ZNF263⟷E2F4 C2H2 ZF⟷E2F 3.27E-41 filter108⟷filter157 LHX5⟷ZNF263 C2H2 ZF⟷Homeodomain 1.30E-40 filter4⟷filter133 E2F1⟷E2F4 E2F⟷E2F 1.39E-40 filter21⟷filter108 DNMT1⟷ZNF263 C2H2 ZF⟷CxxC 2.66E-40 filter3⟷filter4 ZKSCAN1⟷E2F1 C2H2 ZF⟷E2F 3.97E-40 filter4⟷filter80 E2F1⟷TLX2 E2F⟷Homeodomain 4.12E-40 filter18⟷filter190 ZKSCAN1⟷HOXA11 C2H2 ZF⟷Homeodomain 4.74E-40 filter37⟷filter112 ZNF202⟷EGR1 C2H2 ZF⟷C2H2 ZF 5.54E-40 filter18⟷filter108 HOXA11⟷ZNF263 C2H2 ZF⟷Homeodomain 5.80E-40 filter6⟷filter37 SOX3⟷EGR1 C2H2 ZF⟷Sox 1.19E-39 filter4⟷filter21 E2F1⟷DNMT1 E2F⟷CxxC 1.71E-39 filter4⟷filter160 E2F1⟷YBX2 E2F⟷CSD 2.89E-39 filter37⟷filter93 ZNF35⟷EGR1 C2H2 ZF⟷C2H2 ZF 3.35E-39 filter4⟷filter149 E2F1⟷MLL E2F⟷CxxC 1.08E-37 filter21⟷filter190 ZKSCAN1⟷DNMT1 C2H2 ZF⟷CxxC 1.26E-37 filter108⟷filter160 ZNF263⟷YBX2 C2H2 ZF⟷CSD 2.50E-37 filter6⟷filter108 SOX3⟷ZNF263 C2H2 ZF⟷Sox 3.17E-37 filter87⟷filter108 ZNF202⟷ZNF263 C2H2 ZF⟷C2H2 ZF 5.87E-37 filter58⟷filter152 DNMT1⟷SOX1 Sox⟷CxxC 6.01E-37 filter4⟷filter41 E2F1⟷KDM2B E2F⟷CxxC 5.97E-36 filter69⟷filter108 HHEX⟷ZNF263 C2H2 ZF⟷Homeodomain 3.43E-35 filter21⟷filter109 DNMT1⟷HHEX Homeodomain⟷CxxC 3.47E-35 filter37⟷filter154 EGR1⟷DMRTA2 C2H2 ZF⟷DM 8.47E-35 filter4⟷filter93 E2F1⟷ZNF35 C2H2 ZF⟷E2F 1.91E-34 filter4⟷filter114 E2F1⟷ZFY C2H2 ZF⟷E2F 4.69E-34 filter4⟷filter154 E2F1⟷DMRTA2 E2F⟷DM 5.47E-34 filter109⟷filter190 ZKSCAN1⟷HHEX C2H2 ZF⟷Homeodomain 6.49E-34 filter114⟷filter190 ZKSCAN1⟷ZFY C2H2 ZF⟷C2H2 ZF 9.63E-34 filter69⟷filter114 HHEX⟷ZFY C2H2 ZF⟷Homeodomain 1.02E-33 filter18⟷filter109 HOXA11⟷HHEX Homeodomain⟷Homeodomain 1.32E-33 filter53⟷filter178 SRF⟷SP2 C2H2 ZF⟷MADS box 1.92E-33 filter108⟷filter153 ZNF263⟷LCOR C2H2 ZF⟷Pipsqueak 2.03E-33 filter130⟷filter178 ZNF32⟷SP2 C2H2 ZF⟷C2H2 ZF 5.44E-33 filter4⟷filter6 E2F1⟷SOX3 E2F⟷Sox 1.15E-32 filter109⟷filter160 HHEX⟷YBX2 Homeodomain⟷CSD 2.05E-32 filter114⟷filter160 ZFY⟷YBX2 C2H2 ZF⟷CSD 3.14E-32 filter41⟷filter114 KDM2B⟷ZFY C2H2 ZF⟷CxxC 1.05E-31 filter108⟷filter172 MLL⟷ZNF263 C2H2 ZF⟷CxxC 1.06E-31 filter114⟷filter193 SOX1⟷ZFY C2H2 ZF⟷Sox 1.80E-31 filter4⟷filter87 E2F1⟷ZNF202 C2H2 ZF⟷E2F 2.45E-31 filter18⟷filter133 HOXA11⟷E2F4 E2F⟷Homeodomain 2.56E-31 filter109⟷filter133 HHEX⟷E2F4 E2F⟷Homeodomain 2.90E-31 filter53⟷filter108 SRF⟷ZNF263 C2H2 ZF⟷MADS box 4.09E-31 filter118⟷filter178 ZHX1⟷SP2 C2H2 ZF⟷Homeodomain 7.80E-31 filter109⟷filter164 TLX2⟷HHEX Homeodomain⟷Homeodomain 1.20E-30 filter152⟷filter169 DNMT1⟷SIX4 Homeodomain⟷CxxC 1.30E-30 filter109⟷filter193 SOX1⟷HHEX Sox⟷Homeodomain 1.74E-30 filter164⟷filter190 ZKSCAN1⟷TLX2 C2H2 ZF⟷Homeodomain 2.25E-30 filter160⟷filter190 ZKSCAN1⟷YBX2 C2H2 ZF⟷CSD 2.63E-30 filter114⟷filter164 TLX2⟷ZFY C2H2 ZF⟷Homeodomain 4.55E-30 filter109⟷filter149 MLL⟷HHEX Homeodomain⟷CxxC 7.06E-30 filter21⟷filter133 DNMT1⟷E2F4 E2F⟷CxxC 1.03E-29 filter29⟷filter178 CPEB1⟷SP2 Unknown⟷C2H2 ZF 1.38E-29 filter151⟷filter152 DNMT1⟷ZNF35 C2H2 ZF⟷CxxC 1.58E-29 filter162⟷filter190 ZKSCAN1⟷KDM2B C2H2 ZF⟷CxxC 2.22E-29 filter152⟷filter192 TLX2⟷DNMT1 Homeodomain⟷CxxC 4.22E-29 filter133⟷filter190 ZKSCAN1⟷E2F4 C2H2 ZF⟷E2F 7.08E-29 filter149⟷filter190 ZKSCAN1⟷MLL C2H2 ZF⟷CxxC 1.32E-28 filter112⟷filter152 DNMT1⟷ZNF202 C2H2 ZF⟷CxxC 2.47E-28 filter37⟷filter53 EGR1⟷SRF C2H2 ZF⟷MADS box 2.64E-28 filter4⟷filter159 E2F1⟷LHX5 E2F⟷Homeodomain 1.41E-27 filter18⟷filter164 TLX2⟷HOXA11 Homeodomain⟷Homeodomain 1.93E-27 filter108⟷filter130 ZNF263⟷ZNF32 C2H2 ZF⟷C2H2 ZF 2.01E-27 filter168⟷filter178 HOXB13⟷SP2 C2H2 ZF⟷Homeodomain 3.25E-27 filter93⟷filter114 ZNF35⟷ZFY C2H2 ZF⟷C2H2 ZF 3.39E-27 filter54⟷filter152 KDM2B⟷DNMT1 CxxC⟷CxxC 4.33E-27 filter18⟷filter160 HOXA11⟷YBX2 Homeodomain⟷CSD 1.21E-26 filter190⟷filter193 ZKSCAN1⟷SOX1 C2H2 ZF⟷Sox 1.70E-26 filter114⟷filter149 MLL⟷ZFY C2H2 ZF⟷CxxC 1.76E-26 filter21⟷filter160 DNMT1⟷YBX2 CxxC⟷CSD 2.32E-26 filter149⟷filter152 DNMT1⟷MLL CxxC⟷CxxC 3.13E-26 filter4⟷filter17 E2F1⟷SIX4 E2F⟷Homeodomain 1.10E-25 filter114⟷filter154 DMRTA2⟷ZFY C2H2 ZF⟷DM 1.76E-25 filter108⟷filter118 ZNF263⟷ZHX1 C2H2 ZF⟷Homeodomain 4.55E-25 filter41⟷filter109 KDM2B⟷HHEX Homeodomain⟷CxxC 5.07E-25 filter114⟷filter157 LHX5⟷ZFY C2H2 ZF⟷Homeodomain 6.91E-25 filter99⟷filter152 DNMT1⟷LHX5 Homeodomain⟷CxxC 2.55E-24 filter11⟷filter37 GMEB1⟷EGR1 SAND⟷C2H2 ZF 6.06E-24 filter92⟷filter162 KDM2B⟷TLX2 Homeodomain⟷CxxC 6.44E-24 filter6⟷filter152 SOX3⟷DNMT1 Sox⟷CxxC 7.87E-24 filter18⟷filter172 HOXA11⟷MLL Homeodomain⟷CxxC 1.05E-23 filter4⟷filter153 E2F1⟷LCOR E2F⟷Pipsqueak 1.14E-23 filter117⟷filter159 EGR1⟷LHX5 C2H2 ZF⟷Homeodomain 1.51E-23 filter37⟷filter153 EGR1⟷LCOR C2H2 ZF⟷Pipsqueak 1.61E-23 filter4⟷filter11 E2F1⟷GMEB1 E2F⟷SAND 3.46E-23 filter178⟷filter186 SP2⟷FOXK2 C2H2 ZF⟷Forkhead 4.18E-23 filter58⟷filter162 KDM2B⟷SOX1 Sox⟷CxxC 5.82E-23 filter18⟷filter41 HOXA11⟷KDM2B Homeodomain⟷CxxC 1.18E-22 filter33⟷filter109 ZNF202⟷HHEX C2H2 ZF⟷Homeodomain 1.71E-22 filter29⟷filter108 CPEB1⟷ZNF263 Unknown⟷C2H2 ZF 2.10E-22 filter112⟷filter190 ZKSCAN1⟷ZNF202 C2H2 ZF⟷C2H2 ZF 8.08E-22 filter4⟷filter53 E2F1⟷SRF E2F⟷MADS box 1.44E-21 filter37⟷filter118 EGR1⟷ZHX1 C2H2 ZF⟷Homeodomain 3.10E-21 filter109⟷filter154 DMRTA2⟷HHEX DM⟷Homeodomain 3.55E-21 filter93⟷filter162 ZNF35⟷KDM2B C2H2 ZF⟷CxxC 1.18E-20 filter18⟷filter193 HOXA11⟷SOX1 Sox⟷Homeodomain 1.68E-20 filter160⟷filter164 TLX2⟷YBX2 Homeodomain⟷CSD 1.73E-20 filter41⟷filter133 KDM2B⟷E2F4 E2F⟷CxxC 2.60E-20 filter87⟷filter162 KDM2B⟷ZNF202 C2H2 ZF⟷CxxC 3.00E-20 filter152⟷filter168 DNMT1⟷HOXB13 Homeodomain⟷CxxC 7.27E-20 filter11⟷filter178 GMEB1⟷SP2 SAND⟷C2H2 ZF 1.03E-19 filter114⟷filter153 ZFY⟷LCOR C2H2 ZF⟷Pipsqueak 1.37E-19 filter149⟷filter162 KDM2B⟷MLL CxxC⟷CxxC 1.54E-19 filter18⟷filter33 HOXA11⟷ZNF202 C2H2 ZF⟷Homeodomain 1.68E-19 filter152⟷filter153 DNMT1⟷LCOR CxxC⟷Pipsqueak 1.18E-18 filter4⟷filter118 E2F1⟷ZHX1 E2F⟷Homeodomain 1.29E-18 filter4⟷filter130 E2F1⟷ZNF32 C2H2 ZF⟷E2F 2.08E-18 filter41⟷filter160 KDM2B⟷YBX2 CxxC⟷CSD 4.67E-18 filter118⟷filter152 DNMT1⟷ZHX1 Homeodomain⟷CxxC 4.71E-18 filter53⟷filter190 ZKSCAN1⟷SRF C2H2 ZF⟷MADS box 5.36E-18 filter37⟷filter130 EGR1⟷ZNF32 C2H2 ZF⟷C2H2 ZF 5.91E-18 filter53⟷filter152 DNMT1⟷SRF CxxC⟷MADS box 1.88E-17 filter114⟷filter118 ZFY⟷ZHX1 C2H2 ZF⟷Homeodomain 3.62E-17 filter149⟷filter164 TLX2⟷MLL Homeodomain⟷CxxC 5.92E-17 filter25⟷filter114 SOX3⟷ZFY C2H2 ZF⟷Sox 6.25E-17 filter169⟷filter190 SIX4⟷ZKSCAN1 C2H2 ZF⟷Homeodomain 6.52E-17 filter36⟷filter154 MLL⟷DMRTA2 CxxC⟷DM 1.59E-16 filter11⟷filter109 GMEB1⟷HHEX SAND⟷Homeodomain 1.79E-16 filter93⟷filter109 ZNF35⟷HHEX C2H2 ZF⟷Homeodomain 2.75E-16 filter133⟷filter193 SOX1⟷E2F4 E2F⟷Sox 3.19E-16 filter133⟷filter160 E2F4⟷YBX2 E2F⟷CSD 3.96E-16 filter112⟷filter172 ZNF202⟷MLL C2H2 ZF⟷CxxC 7.14E-16 filter29⟷filter152 CPEB1⟷DNMT1 Unknown⟷CxxC 8.20E-16 filter133⟷filter172 MLL⟷E2F4 E2F⟷CxxC 8.58E-16 filter160⟷filter193 SOX1⟷YBX2 Sox⟷CSD 1.60E-15 filter4⟷filter29 E2F1⟷CPEB1 E2F⟷Unknown 1.63E-15 filter11⟷filter190 GMEB1⟷ZKSCAN1 SAND⟷C2H2 ZF 3.29E-15 filter160⟷filter172 MLL⟷YBX2 CxxC⟷CSD 3.65E-15 filter118⟷filter162 ZHX1⟷KDM2B Homeodomain⟷CxxC 5.81E-15 filter27⟷filter109 LHX5⟷HHEX Homeodomain⟷Homeodomain 9.29E-15 filter154⟷filter190 DMRTA2⟷ZKSCAN1 C2H2 ZF⟷DM 2.55E-14 filter18⟷filter27 HOXA11⟷LHX5 Homeodomain⟷Homeodomain 3.24E-14 filter33⟷filter133 ZNF202⟷E2F4 C2H2 ZF⟷E2F 4.17E-14 filter112⟷filter143 ZNF202⟷SOX1 C2H2 ZF⟷Sox 6.22E-14 filter23⟷filter112 TLX2⟷ZNF202 C2H2 ZF⟷Homeodomain 7.50E-14 filter153⟷filter162 LCOR⟷KDM2B CxxC⟷Pipsqueak 1.33E-13 filter25⟷filter109 SOX3⟷HHEX Sox⟷Homeodomain 3.25E-13 filter18⟷filter53 HOXA11⟷SRF Homeodomain⟷MADS box 3.97E-13 filter112⟷filter118 ZNF202⟷ZHX1 C2H2 ZF⟷Homeodomain 4.29E-13 filter53⟷filter109 SRF⟷HHEX Homeodomain⟷MADS box 4.52E-13 filter93⟷filter190 ZKSCAN1⟷ZNF35 C2H2 ZF⟷C2H2 ZF 7.56E-13 filter112⟷filter151 ZNF35⟷ZNF202 C2H2 ZF⟷C2H2 ZF 8.08E-13 filter27⟷filter190 LHX5⟷ZKSCAN1 C2H2 ZF⟷Homeodomain 8.56E-13 filter11⟷filter21 GMEB1⟷DNMT1 SAND⟷CxxC 3.47E-12 filter25⟷filter190 SOX3⟷ZKSCAN1 C2H2 ZF⟷Sox 3.76E-12 filter53⟷filter162 SRF⟷KDM2B CxxC⟷MADS box 3.81E-11 filter6⟷filter112 SOX3⟷ZNF202 C2H2 ZF⟷Sox 2.44E-10 filter17⟷filter112 SIX4⟷ZNF202 C2H2 ZF⟷Homeodomain 2.83E-10 filter25⟷filter162 SOX3⟷KDM2B Sox⟷CxxC 3.09E-10 filter112⟷filter157 ZNF202⟷LHX5 C2H2 ZF⟷Homeodomain 9.57E-10 filter25⟷filter36 SOX3⟷MLL Sox⟷CxxC 5.84E-09 filter11⟷filter160 GMEB1⟷YBX2 SAND⟷CSD 6.67E-09 filter33⟷filter154 ZNF202⟷DMRTA2 C2H2 ZF⟷DM 1.25E-08 filter18⟷filter25 HOXA11⟷SOX3 Sox⟷Homeodomain 1.86E-08 filter90⟷filter176 MLL⟷SOX1 Sox⟷CxxC 4.82E-08 filter12⟷filter193 TLX2⟷SOX1 Sox⟷Homeodomain 6.39E-08 filter99⟷filter162 LHX5⟷KDM2B Homeodomain⟷CxxC 6.54E-08 filter9⟷filter133 TLX2⟷E2F4 E2F⟷Homeodomain 9.00E-08 filter11⟷filter87 GMEB1⟷ZNF202 SAND⟷C2H2 ZF 1.58E-07 filter36⟷filter130 MLL⟷ZNF32 C2H2 ZF⟷CxxC 2.25E-07 filter36⟷filter99 MLL⟷LHX5 Homeodomain⟷CxxC 3.53E-07 filter93⟷filter164 TLX2⟷ZNF35 C2H2 ZF⟷Homeodomain 4.95E-07 filter46⟷filter190 IRF4⟷ZKSCAN1 IRF⟷C2H2 ZF 5.24E-07 filter11⟷filter133 GMEB1⟷E2F4 E2F⟷SAND 6.10E-07 filter53⟷filter133 SRF⟷E2F4 E2F⟷MADS box 6.37E-07 filter19⟷filter36 ZNF35⟷MLL C2H2 ZF⟷CxxC 1.51E-06 filter133⟷filter154 E2F4⟷DMRTA2 E2F⟷DM 2.31E-06 filter157⟷filter164 TLX2⟷LHX5 Homeodomain⟷Homeodomain 3.30E-06 filter17⟷filter92 SIX4⟷TLX2 Homeodomain⟷Homeodomain 1.03E-05 filter53⟷filter92 SRF⟷TLX2 Homeodomain⟷MADS box 2.78E-05 filter67⟷filter171 DMRTA2⟷TLX2 DM⟷Homeodomain 4.83E-05 filter93⟷filter133 ZNF35⟷E2F4 C2H2 ZF⟷E2F 0.00013233 filter11⟷filter164 GMEB1⟷TLX2 SAND⟷Homeodomain 0.000149951 filter6⟷filter171 SOX3⟷TLX2 Sox⟷Homeodomain 0.000158071 filter112⟷filter168 ZNF202⟷HOXB13 C2H2 ZF⟷Homeodomain 0.000173773 filter153⟷filter190 LCOR⟷ZKSCAN1 C2H2 ZF⟷Pipsqueak 0.000691234 filter25⟷filter160 SOX3⟷YBX2 Sox⟷CSD 0.001053489 filter33⟷filter153 ZNF202⟷LCOR C2H2 ZF⟷Pipsqueak 0.002097638 filter54⟷filter169 KDM2B⟷SIX4 Homeodomain⟷CxxC 0.002703067 filter59⟷filter153 HHEX⟷LCOR Homeodomain⟷Pipsqueak 0.004476314 filter153⟷filter172 LCOR⟷MLL CxxC⟷Pipsqueak 0.004838783 filter18⟷filter153 HOXA11⟷LCOR Homeodomain⟷Pipsqueak 0.007341989 filter11⟷filter149 GMEB1⟷MLL SAND⟷CxxC 0.007618156 filter11⟷filter53 GMEB1⟷SRF SAND⟷MADS box 0.008502348 filter29⟷filter92 CPEB1⟷TLX2 Unknown⟷Homeodomain 0.010610237 filter92⟷filter153 TLX2⟷LCOR Homeodomain⟷Pipsqueak 0.011377339 filter171⟷filter186 TLX2⟷FOXK2 Homeodomain⟷Forkhead 0.016972013 filter118⟷filter142 ZHX1⟷TLX2 Homeodomain⟷Homeodomain 0.018359505 filter133⟷filter153 E2F4⟷LCOR E2F⟷Pipsqueak 0.025412032 filter53⟷filter199 SRF⟷IRX4 Homeodomain⟷MADS box 0.029247405 filter111⟷filter169 SOX1⟷SIX4 Sox⟷Homeodomain 0.041477178