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Large-scale Analysis of Recurrent Variants in Annotations (LARVA)
ANNOTATION DATA README FILE

LARVA version 2.0
July 15, 2015

Lucas Lochovsky	and Jing Zhang
Gerstein Lab
Yale University
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List of annotation files in "noncoding-annotations" directory:

1) DHS_sites.bed: Dnase I hypersensitive sites derived from the ENCODE project.
Source: genome.ucsc.edu/ENCODE

2) DRM.bed: Distal regulatory module (DRM) enhancers, which regulate the expression of genes at non-adjacent sites.
Source: PMID 22950945

3) gencode.v16.promoter.bed: Promoter annotations derived from GENCODE v16.
Source: gencodegenes.org

4) gencode.v16.utr.bed: UTR annotations derived from GENCODE v16.
Source: gencodegenes.org

5) TF_binding_sites.bed: Transcription factor binding sites derived from the ENCODE project.
Source: genome.ucsc.edu/ENCODE

6) tss.bed: Transcription start sites derived by taking the 100bp intervals immediately upstream of all GENCODE coding gene annotations.
Source: gencodegenes.org

7) ultra-conserved.bed: Sites that are highly conserved across many phylogenetic branches.
Source: PMID 15131266

8) ultra-sensitive.bed: Noncoding regions under higher selective pressure than most other noncoding regions.
Source: PMID 24092746