dREG Gateway

Welcome to dREG and dTOX gateway!

Find the location of enhancers and promoters using PRO-seq, GRO-seq, and ChRO-seq data.

The gateway status and updates are here!


How is dREG used?

The dREG model in the gateway predicts the location of enhancers and promoters using PRO-seq, GRO-seq, or ChRO-seq data. The server takes as input bigWig files provided by the user, which represent PRO-seq signal on the plus and minus strand. The gateway uses pre-trained dREG model to identify divergent transcript start sites and impute the predicted DNase-1 hypersensitivity signal across the genome. The current dREG model works in any mammalian organism.

Registered users need only upload experimental data in the required format and push the start button. Once the job is finished, the user will be notified by e-mail. Results can be downloaded to the user’s local machine, or viewed in the Genome Browser via the handy trackhub link.

Use the Danko lab's mapping pipeline (here) to prepare bigWig files from fastq files or convert BAM files of mapped reads to bigWig (here).

See our FAQ, documentation or dREG protocol manuscript for additional questions.

dREG model

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How is dTOX used?

Under construction, please ignore this section!

The dTOX models in the gateway predict the binding status of transcription factor binding sites using PRO-seq, ATAC-seq, or DNase-1-seq data. The server takes as input bigWig files provided by the user, which represent the PRO-seq, ATAC-seq, or DNase-1-seq signal on the plus and minus strand. Once the user selects the transcription factors to predict on, the gateway uses a pre-trained dTOX model to identify transcription factor binding patterns. The current dTOX models work in any mammalian organism and on any motif that has an associated position-weight matrix.

The web operations are same as the dREG model. Users need to login -> upload data -> run data. Results can be downloaded or viewed in the WashU Genome browser.

See our FAQ, documentation for additional questions.

dREG model

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Gateway Introduction

The dREG gateway is a cloud platform developed by the Danko lab at the Baker Institute, Cornell University and supported by the SciGap (Science Gateway Platform as a Service) and XSEDE (Extreme Science and Engineering Discovery Environment).

Currently, this gateway hosts two bioinformatics services for functional analysis of sequencing data, dREG transcriptional regulatory element peak calling and dTOX transcription factor binding prediction. Both services take as input files (either PRO-seq, GRO-seq, ATAC-seq or DNase-1-seq) provided by the user, and then uses pre-trained models to conduct prediction and post-processing on GPU computing nodes. The architecture and details are here.

Publications

dREG model

Danko, C. G., Hyland, S. L., Core, L. J., Martins, A. L., Waters, C. T., Lee, H. W., ... & Siepel, A. (2015). Identification of active transcriptional regulatory elements from GRO-seq data. Nature methods, 12(5), 433-438.

dREG model

Wang, Z., Chu, T., Choate, L. A., & Danko, C. G. (2018). Identification of regulatory elements from nascent transcription using dREG. bioRxiv, 321539.