Sequence-conserved Enhancer-like Elements

The present repository contains the sequence-conserved enhancer-like elements (ELEs) identified in 106 human tissues and cell types and the corresponding source codes.

If you find any part of this repository useful for your work, please kindly cite the following research article:

Zhu, X., Ma, S. & Wong, W.H. Genetic effects of sequence-conserved enhancer-like elements on human complex traits. Genome Biol 25, 1 (2024). https://doi.org/10.1186/s13059-023-03142-1

Correspondence should be addressed to X.Z. (xiangzhu[at]psu.edu) and W.H.W (whwong[at]stanford.edu).

Source Data

The data folder provides the source data of this study. The MD5 hash of each file is provided to help users verify the file integrity.

The omnibus_bed.zip file provides the following files.

Name	Description
merge_human.bed	Omnibus ELEs
merge_human_mouse_01.bed	Lowly-conserved (LC) omnibus ELEs
merge_human_mouse_05.bed	Moderately-conserved (MC) omnibus ELEs
merge_human_mouse_09.bed	Highly-conserved (HC) omnibus ELEs

Each row of each BED file in omnibus_bed.zip defines an omnibus ELE, indicated by the chromosome, start and end positions.

$ head -n 1 omnibus_bed/merge_human_mouse_09.bed
chr1	746181	746729

The context_specific_bed.zip file provides the following files.

Name	Description
human.bed	Context-specific ELEs
human_mouse_01.bed	LC context-specific ELEs
human_mouse_05.bed	MC context-specific ELEs
human_mouse_09.bed	HC context-specific ELEs

Each row of each BED file in context_specific_bed.zip defines an ELE together with the tissue or cell type from which it is derived. For example, chr1:1167581-1168822 shown below is a HC context-specific ELE derived from the A549 cell line.

$ head -n 1 context_specific_bed/human_mouse_09.bed
chr1	1167581	1168822	A549

All the BED files are based on the GRCh37 (hg19) genome assembly.

Source Codes

The code folder provides the source codes of this study, as well as a real-world example showing how to use the codes. The MD5 hash of each file related to this example is provided to help users verify the file integrity.

Our method requires the BED files of human H3K27ac and chromatin accessibility peaks identified in the same context as input. For example, the code/input folder provides the BED files of H3K27ac and chromatin accessibility identified in embryonic large intestine.

Name	Description
hg19_ac_large_intestine_embryo_ENCFF906VKA.bed	H3K27ac peaks
hg19_open_large_intestine_embryo_ENCFF276FKY.bed	Chromatin accessibility peaks

The code/example.sh takes the BED files of human H3K27ac and chromatin accessibility peaks as input, and produces the ELEs with sequence conservation (LC, MC, HC) in the same context. For example, the code/output folder provides the output sequence-conserved ELEs for human embryonic large intestine.

Name	Description
hg19_mm10_01_hg19_large_intestine_embryo_ac_open.bed	LC context-specific ELEs
hg19_mm10_05_hg19_large_intestine_embryo_ac_open.bed	MC context-specific ELEs
hg19_mm10_09_hg19_large_intestine_embryo_ac_open.bed	HC context-specific ELEs

The code/intermediate folder consists of intermediate files that are produced by code/example.sh.