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Deep neural networks identify sequence context features predictive of transcription factor binding

Nature Machine Intelligence volume 3, pages 172–180 (2021)Cite this article

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A preprint version of the article is available at bioRxiv.

Abstract

Transcription factors bind DNA by recognizing specific sequence motifs, which are typically 6–12 bp long. A motif can occur many thousands of times in the human genome, but only a subset of those sites are actually bound. Here we present a machine-learning framework leveraging existing convolutional neural network architectures and model interpretation techniques to identify and interpret sequence context features most important for predicting whether a particular motif instance will be bound. We apply our framework to predict binding at motifs for 38 transcription factors in a lymphoblastoid cell line, score the importance of context sequences at base-pair resolution and characterize context features most predictive of binding. We find that the choice of training data heavily influences classification accuracy and the relative importance of features such as open chromatin. Overall, our framework enables novel insights into features predictive of transcription factor binding and is likely to inform future deep learning applications to interpret non-coding genetic variants.

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Fig. 1: AgentBind overview.
Fig. 2: Interpreting context-specific determinants of TF binding.
Fig. 3: Identifying key context sequence features for TF binding in GM12878.
Fig. 4: Cell-type-specific enrichment of 5-mers influential for STAT3 binding.

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Data availability

Variant annotation scores for each TF analysed can be found at https://github.com/Pandaman-Ryan/AgentBind. Peak files for ENCODE ChIP-seq datasets can be found at http://hgdownload.cse.ucsc.edu/goldenpath/hg19/encodeDCC/wgEncodeAwgTfbsUniform. Peak files for STAT3 in CD4+ T cells were obtained from the Gene Expression Omnibus (GEO accession GSM2545819).

Code availability

Code used for training models and performing analyses are available in our Github repository https://github.com/Pandaman-Ryan/AgentBind (ref. 45)

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Acknowledgements

This study was supported in part by NIH/NHGRI 1R21HG010070-01 (M.G.), the Microsoft Genomics for Research programme and an Amazon Web Services research award. We thank NVIDIA for donating a Tesla K40 GPU to support this project. We additionally thank C. Benner, C. Glass and A. Goren for helpful comments.

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Authors and Affiliations

  1. Department of Computer Science and Engineering, University of California San Diego, La Jolla, CA, USA

    An Zheng, Hao Su & Melissa Gymrek

  2. Department of Bioengineering, University of California San Diego, La Jolla, CA, USA

    Michael Lamkin

  3. Department of Biological Sciences, University of California San Diego, La Jolla, CA, USA

    Hanqing Zhao

  4. Bioinformatics and Systems Biology Program, University of California San Diego, La Jolla, CA, USA

    Cynthia Wu

  5. Department of Medicine, University of California San Diego, La Jolla, CA, USA

    Melissa Gymrek

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Contributions

A.Z. designed and performed analyses and helped write the manuscript. M.L., H.Z. and C.W. helped perform analyses. H.S. helped design the study. M.G. conceived the study, supervised analyses and helped write the manuscript.

Corresponding author

Correspondence to Melissa Gymrek.

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The authors declare no competing interests.

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Peer review information Nature Machine Intelligence thanks David Gifford, Peter Koo and the other, anonymous, reviewer(s) for their contribution to the peer review of this work.

Publisher’s note Springer Nature remains neutral with regard to jurisdictional claims in published maps and institutional affiliations.

Extended data

Extended Data Fig. 1 Model performance related to GC content and open chromatin.

(a,b) GC content differences correlated with model performance. The x-axis shows the absolute value of the difference in mean GC content for positive vs. negative sequences with the motif for each TF. The y-axis shows auROCs. Each dot represents one TF. Results in a-b are for baseline models with motifs blocked (a) or unblocked (b). (c) Comparison of training data size and change in model performance. The x-axis (log10 scale) shows the number of training samples. Orange points show the difference in auROC (y-axis) for baseline vs. GC-controlled models. Green points show GC-controlled vs. DNase-I-controlled models. Each dot represents one TF. (d) Model performance for each TF. The y-axis gives the auROC obtained for different models for each TF. Grey = baseline; orange = GC-controlled; green = DNase-I-controlled. TFs are ranked by the change in auROC between the DNase-I and GC-controlled models. (e) Comparison of cross-TF model performance. Heatmaps show the auROC using a GC-controlled model trained on one TF (rows) and tested on another TF (columns). Red squares denote the model with highest auROC for each TF. (f) Distribution of the difference in auROC between top models and TF-specific models. For TFs where the TF-specific model was best, we computed the difference between the TF-specific model and the next best model (red). For all other TFs, we compared performance of the best model to the TF-specific model (blue). (g-h) are the same as in e-f but based on DNase-I-controlled models.

Extended Data Fig. 2 Aggregate Grad-CAM score profiles for each TF.

For each TF, we computed the average absolute value of the Grad-CAM score per position using either models with the core motif unblocked (left) or blocked (right). Values shown are Z-normalized across rows. (a) shows aggregate scores for sequences labelled as positive (bound) and is reproduced from Fig. 2d. (b) shows aggregate scores for sequences labelled as negative (unbound).

Extended Data Fig. 3 Comparing key context sequence features identified in pre-trained vs. fine-tuned models.

The heatmap shows the enrichment of each 5-mer in regions with the highest Grad-CAM scores for each TF using baseline models before (a) and after (b) fine-tuning. Rows and columns are ordered the same as in Fig. 3. Colours denote odds ratios and the sizes of the boxes denote statistical significance as in Fig. 3. Panel (b) is reproduced from Fig. 3a for comparison.

Extended Data Fig. 4 Context sequence features specific to proximal vs. distal sites.

(a) Enrichment of 5-mers in high-scoring Grad-CAM regions for proximal (left) and distal (right) binding sites. Proximal and distal TF binding sites are defined as described in Methods. Rows and columns are ordered the same as in Fig. 3. (b,c) are the same as in (a) but show data for GC-controlled (b) and DNase-I-controlled (c) models. For (a–c), colours denote odds ratios and the sizes of the boxes denote statistical significance as in Fig. 3. (d) Comparison of top scoring 5-mers in proximal vs. distal SP1 sites. Bars show the odds ratio of enrichment of each sequence in top 5-mers for all (gray), proximal (red) and distal (blue) SP1 sites. The top 20 5-mers ranked by the best odds ratio across all three SP1 models (all, proximal, and distal sites) are shown. Error bars show 95% confidence intervals on odds ratios. (e,f) are the same as in (d) but show data for GC-controlled (e) and DNase-I-controlled (f) models.

Extended Data Fig. 5 Singleton rate of context SNPs vs. core motif regions.

(a) Singleton rate of context SNPs. The plot shows the percent of SNPs in each category that are singletons. Black = all context sites, orange = context sites with top 5% Grad-CAM scores, red = context sites with top 0.5% Grad-CAM scores. Error bars show +/− 1 s.e. (b) is the same as (a), but additionally shows singleton rates for SNPs in core motif regions (blue). The number of SNPs in each category for each TF is annotated above each plot.

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Zheng, A., Lamkin, M., Zhao, H. et al. Deep neural networks identify sequence context features predictive of transcription factor binding. Nat Mach Intell 3, 172–180 (2021). https://doi.org/10.1038/s42256-020-00282-y

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