Functional Conservation of DNA Elements (FUNCODE)

Scripts for computing FUNCODE scores from ENCODE DNase-seq, ATAC-seq and Histoen ChIP-seq data.

UCSC Browser track hubs:

hg38 mm10

Output types on ENCODE data portal

These scripts produce data corresponding to two output types on the ENCODE data portal:

(1) "functional conservation quantification"

(2) "functional conservation mapping".

• "functional conservation mapping" is relevant if the user would like to map regulatory elements across species.

The following datasets contain "functional conservation mapping":

Accession	Description
ENCSR174NMF	FUNCODE conservation scores of context-dependent variable acitivity (CO-V) for chromatin accessibility at human(hg38)-mouse(mm10) DHS pairs derived from nearby gene homology
ENCSR079JCW	FUNCODE conservation scores of context-dependent variable acitivity (CO-V) for H3K27ac histone modification at human(hg38)-mouse(mm10) DHS pairs derived from nearby gene homology
ENCSR799PIS	FUNCODE conservation scores of context-dependent variable acitivity (CO-V) for H3K4me1 histone modification at human(hg38)-mouse(mm10) DHS pairs derived from nearby gene homology
ENCSR241JXZ	FUNCODE conservation scores of context-dependent variable acitivity (CO-V) for H3K4me3 histone modification at human(hg38)-mouse(mm10) DHS pairs derived from nearby gene homology
ENCSR705SNU	FUNCODE conservation scores of baseline (CO-B) and context-dependent variable activity (CO-V) for chromatin accessibility, H3K27ac, H3K4me1, H3K4me3 at human(hg38)-mouse(mm10) DHS pairs derived from sequence alignment

• "functional conservation quantification" is relevant if the user would like to visualize the functional conservation signal in either human or mouse genome. Both '.bed' and '.bigWig' files are provided.

The following datasets contain "functional conservation quantification":

Accession	Description
ENCSR666RQQ	FUNCODE conservation scores of baseline activity (CO-B) for chromatin accessibility at human DHSs (hg38) paired to mouse using sequence alignment
ENCSR383DSZ	FUNCODE conservation scores of baseline activity (CO-B) for chromatin accessibility at mouse DHSs (mm10) paired to human using sequence alignment
ENCSR794MIL	FUNCODE conservation scores of baseline activity (CO-B) for H3K27ac histone modification at human DHSs (hg38) paired to mouse using sequence alignment
ENCSR468BFL	FUNCODE conservation scores of baseline activity (CO-B) for H3K27ac histone modification at mouse DHSs (mm10) paired to human using sequence alignment
ENCSR166FHJ	FUNCODE conservation scores of baseline activity (CO-B) for H3K4me1 histone modification at human DHSs (hg38) paired to mouse using sequence alignment
ENCSR312OMI	FUNCODE conservation scores of baseline activity (CO-B) for H3K4me1 histone modification at mouse DHSs (mm10) paired to human using sequence alignment
ENCSR623QIK	FUNCODE conservation scores of baseline activity (CO-B) for H3K4me3 histone modification at human DHSs (hg38) paired to mouse using sequence alignment
ENCSR840YRP	FUNCODE conservation scores of baseline activity (CO-B) for H3K4me3 histone modification at mouse DHSs (mm10) paired to human using sequence alignment
ENCSR289SXF	FUNCODE conservation scores of context-dependent variable activity (CO-V) for chromatin accessibility at human DHSs (hg38) paired to mouse using sequence alignment
ENCSR989MYS	FUNCODE conservation scores of context-dependent variable activity (CO-V) for chromatin accessibility at mouse DHSs (mm10) paired to human using sequence alignment
ENCSR542FJK	FUNCODE conservation scores of context-dependent variable activity (CO-V) for H3K27ac histone modification at human DHSs (hg38) paired to mouse using sequence alignment
ENCSR981BVO	FUNCODE conservation scores of context-dependent variable activity (CO-V) for H3K27ac histone modification at mouse DHSs (mm10) paired to human using sequence alignment
ENCSR825SLF	FUNCODE conservation scores of context-dependent variable activity (CO-V) for H3K4me1 histone modification at human DHSs (hg38) paired to mouse using sequence alignment
ENCSR275KOD	FUNCODE conservation scores of context-dependent variable activity (CO-V) for H3K4me1 histone modification at mouse DHSs (mm10) paired to human using sequence alignment
ENCSR012VAU	FUNCODE conservation scores of context-dependent variable activity (CO-V) for H3K4me3 histone modification at human DHSs (hg38) paired to mouse using sequence alignment
ENCSR811LNW	FUNCODE conservation scores of context-dependent variable activity (CO-V) for H3K4me3 histone modification at mouse DHSs (mm10) paired to human using sequence alignment
ENCSR193MVK	FUNCODE conservation scores of context-dependent variable activity (CO-V) for chromatin accessibility at human DHSs (hg38) paired to mouse using nearby gene homology
ENCSR785AKM	FUNCODE conservation scores of context-dependent variable activity (CO-V) for chromatin accessibility at mouse DHSs (mm10) paired to human using nearby gene homology
ENCSR024SYD	FUNCODE conservation scores of context-dependent variable activity (CO-V) for H3K27ac histone modification at human DHSs (hg38) paired to mouse using nearby gene homology
ENCSR389ESN	FUNCODE conservation scores of context-dependent variable activity (CO-V) for H3K27ac histone modification at mouse DHSs (mm10) paired to human using nearby gene homology
ENCSR211HIA	FUNCODE conservation scores of context-dependent variable activity (CO-V) for H3K4me1 histone modification at human DHSs (hg38) paired to mouse using nearby gene homology
ENCSR786OQS	FUNCODE conservation scores of context-dependent variable activity(CO-V) for H3K4me1 histone modification at mouse DHSs (mm10) paired to human using nearby gene homology
ENCSR760RUZ	FUNCODE conservation scores of context-dependent variable activity (CO-V) for H3K4me3 histone modification at human DHSs (hg38) paired to mouse using nearby gene homology
ENCSR168ZNZ	FUNCODE conservation scores of context-dependent variable activity (CO-V) for H3K4me3 histone modification at mouse DHSs (mm10) paired to human using nearby gene homology

Details:

To reproduce the FUNCODE scores, use the following steps:

1. Generate pairs of mapped DHS elements based on pairwsie sequence alignment (UCSC Blastz)

2. Download and process sequence read alignment files (bam) from ENCODE data portal

3. Integrate data between human and mouse

4. Compute FUNCODE CO-V and CO-B scores for sequence alignable DHS pairs

5. Compute FUNCODE CO-V scores for sequence DHS pairs with nearby gene homology, and calls significantly conserved pairs

For details on each step, see README in the corresponding sub-directories.

Report bugs and provide suggestions by sending email to:

Author and maintainer: Weixiang Fang ([email protected])

Contributers: Chaoran Chen, Boyang Zhang