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).
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 746729The 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 A549All the BED files are based on the GRCh37 (hg19) genome assembly.
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.