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