BIRD-data: a dataset for big data prediction

This repository contains the preprocessed training datasets used for BIRD(Big data Regression for predicting DNase I hypersensitivity). It contains two types of genomic data: chromatin accessibility (DNase-seq) and gene expression (Exon array or RNA-seq). The reference genome for these datasets is huamn genome hg19.

There are three training datasets:

1. DNase-seq and Exon array data from the previous ENCODE project for 57 samples.
2. DNase-seq and RNA-seq data from the Epigenome Roadmap project for 70 samples.
3. DNase-seq and RNA-seq data from the current ENCODE project for 167 samples.

These datasets can also be useful for testing other machine learning algorithms in the context of genomics. For more details about the prediction problems in genomics, please check the following papers:

Zhou W, Sherwood B, Ji Z, Xue Y, Du F, Bai J, Ying M, Ji H. Genome-wide Prediction of DNase I Hypersensitivity Using Gene Expression. Nature Communications 8, 1038 (2017). (open access)

Zhou W, Sherwood B, Ji H. Computational Prediction of the Global Functional Genomic Landscape: Applications, Methods, and Challenges. Human Heredity 81, 88-105 (2016). (author manuscript)

Download the data

The data can be downloaded via the following links:

DNase-seq and Exon array data from the previous ENCODE project for 57 samples: https://github.com/WeiqiangZhou/BIRD-data/releases/download/v1.0/BIRD_data.zip

DNase-seq and RNA-seq data from the Epigenome Roadmap project for 70 samples: https://github.com/WeiqiangZhou/BIRD-data/releases/download/v2.0/BIRD_data_Roadmap.zip

DNase-seq and RNA-seq data from the current ENCODE project for 167 samples: https://github.com/WeiqiangZhou/BIRD-data/releases/download/v3.0/BIRD_data_ENCODE.zip

Chromatin accessibility data

To load the data, use the follow command in R.

DNase_57_cells <- readRDS("DNase_data_57_cells.rds")
DNase_70_cells <- readRDS("DNase_data_70_cells.rds")
DNase_167_cells <- readRDS("DNase_data_167_cells.rds")

The first three columns in the data contains the location information of a genomic locus (200bp window). For other columns, each column is a cell type and each row is a genomic locus. The value represents the normalized and log-transformed DNase-seq signal.

Gene expression data

To load the data, use the following command:

Exon_57_cells <- readRDS("Exon_data_57_cells.rds")
RNA_70_cells <- readRDS("RNA_data_70_cells.rds")
RNA_167_cells <- readRDS("RNA_data_167_cells.rds")

The rownames of the data contains the "transcript cluster id" of each gene in the exon array data or the ensembl gene id of each gene in the RNA-seq data. For the exon array data, please check the annotation data. Each column is a cell type and each row is a gene. The value represents the quantile normalized and log transformed gene expression.

The prediction problem

Let the chromatin accessibility data be Y and the gene expression data be X. The problem can be formulated as how to predict Y using X.

Other files in the dataset

There are three other txt files in the dataset ("DH_cluster_1000.txt", "DH_cluster_2000.txt", and "DH_cluster_5000.txt"). These files contain the membership of the clustering result for the genomic loci (rows) using 1000, 2000, or 5000 clusters based on the chromatin accessibility data (Y).

Citations

The raw data for this dataset is obtained from ENCODE and processed as described in BIRD. Please cite the ENCODE paper, Epigenome Roadmap paper, and the BIRD paper if you used this dataset.

ENCODE Project Consortium. An integrated encyclopedia of DNA elements in the human genome. Nature 489, 57–74 (2012). (open access)

Roadmap Epigenomics Consortium. Integrative analysis of 111 reference human epigenomes. Nature, 518, 317–330 (2015). (open access)

Zhou W, Sherwood B, Ji Z, Xue Y, Du F, Bai J, Ying M, Ji H. Genome-wide Prediction of DNase I Hypersensitivity Using Gene Expression. Nature Communications 8, 1038 (2017). (open access)