Integrative analysis across 3,604 GWAS reveals multiple novel cell type-specific regulatory associations

This dataset contains files associated with the manuscript "Integrative analysis across 3,604 GWAS reveals multiple novel cell type-specific regulatory associations". This manuscript presents Functional element Overlap analysis of the Results of GWAS Experiments 2 (FORGE2), a new method for detecting key phenotype-associated tissues, cell types and regulatory elements using GWAS summary statistics. This manuscript also presents FORGE2 results across several thousand GWAS.

FORGE2 code (as of 22 November 2021) is contained in the compressed folder FORGE2.zip.

FORGE2 code is also contained on GitHub at https://github.com/charlesbreeze/FORGE2

The main figures for the FORGE2 paper, covering the main elements of FORGE2 analysis and results, are:

Figure1.forge2.DHS.pdf

Figure2.forge2.histone.marks.pdf

Figure3.histone.mark.comparison.pdf

Figure4.forge2.chr.states.pdf

Figure5.forge2.relationship.between.marks.pdf

Figure6.example.analysis.figure.pdf

Legends for all figures and tables are included in the file FORGE2.legends.for.figures.and.tables.pdf

The supplementary figures for the FORGE2 paper, covering additional elements of FORGE2 analysis and results, are:

FigureS1.pdf

FigureS2.erc.pdf

FigureS3.encode.pdf

FigureS4.blueprint.pdf

FigureS5.H3K4me1.pdf

FigureS6.H3K4me3.pdf

FigureS7.H3K36me3.pdf

FigureS8.H3K27me3.pdf

FigureS9.H3K9me3.pdf

FigureS10.upset.plot.histone.marks.pdf

FigureS11.TssA.pdf

FigureS12.TssAFlnk.pdf

FigureS13.TssBiv.pdf

FigureS14.Tx.pdf

FigureS15.TxFlnk.pdf

FigureS16.TxWk.pdf

FigureS17.ZNF-Rpts.pdf

FigureS18.BivFlnk.pdf

FigureS19.Enh.pdf

FigureS20.EnhBiv.pdf

FigureS21.EnhG.pdf

FigureS22.Het.pdf

FigureS23.Quies.pdf

FigureS24.ReprPC.pdf

FigureS25.ReprPCWk.pdf

FigureS26.upset.plot.chromatin.states.pdf

The supplementary tables for the FORGE2 paper, with additional data regarding FORGE2 analysis and results, are:

Table.S1.erc2.DHS.xlsx

Table.S2.erc.xlsx

Table.S3.encode.xlsx

Table.S4.blueprint.xlsx

Table.S5.H3K4me1.xlsx

Table.S6.H3K4me3.xlsx

Table.S7.H3K36me3.xlsx

Table.S8.H3K27me3.xlsx

Table.S9.H3K9me3.xlsx

Table.S10.chrstate15.xlsx

Table.S11.MPNs_example.analysis.forge2.h3.all.xlsx

Table.S12.MPNs_example.analysis.forge2.dhs.xlsx