Immune Atlas
Data. This page provides links to raw and processed data sets from
our paper with the Criswell, Marson and Greenleaf labs on
chromatin accessibility and allele-specific effects across diverse
immune cell types: [Calderon et al 2019, Nature Genetics]
SDS is an approach for studying very recent changes in allele frequencies
within a population, using whole genome sequence data. Applied to data
from the UK10K Project (3000 individuals) we estimate that SDS reflects
frequency changes during the past 2,000 years. Large changes in
frequencies imply adaptive events. The software was developed by Yair Field,
and the paper was jointly written by Yair, Evan Boyle, and Natalie Telis.
[software]
[preprint]
[SDS values in UK10K]
Duplicate gene data. Summary data from the
paper
by Lan and Pritchard (2016) on
the evolution of expression in duplicate genes are available here:
[data].
eQTL Web
Site. This website includes data from our projects on QTL mapping in human lymphoblastoid
cells using RNA-seq, DNase-seq and other techniques [Pickrell et al 2010], as well as
a browser summarizing results from a collection of published eQTL studies. It also includes some
scripts for RNA-seq analysis.
Centipede Web Site.
CENTIPEDE is a method developed by Roger Pique-Regi and Jacob Degner
that uses PWM information plus experimental data such as DNase1,
histone marks or FAIRE to infer transcription factor binding sites
with high specificity.
Haplotter Web
Site. A web-browser for checking for signals of
selection in the human genome based on the Phase II HapMap data. See
Voight et al (2006) PLoS Biology. A map of recent positive
selection in the human genome. [PDF]
HGDP Selection Web
Site. A web-browser for checking for signals of
selection in the human genome based on SNP data collected by
Li et al (2008) in the 53 populations that constitute the Human
Genome Diversity Panel. The website also includes scripts for computing
iHS and XP-EHH. This work was reported by Pickrell et al (2009)
and Coop et al
(2009).
Conserved Non-Coding Elements (CNC) Data
used by Kim and Pritchard (2007) PloS Genetics. Adaptive evolution of conserved non-coding elements in mammals. [PDF]
SNP data (2834 sites, 52 worldwide populations)
used by Conrad et al (2006) Nature Genetics. A worldwide survey of
haplotype variation and linkage disequilibrium in the human
genome. [PDF]
[Rosenberg diversity panel website]
Microsatellite data (377 loci, 52 worldwide
populations) used by Rosenberg, Pritchard et al (2002) Science. Genetic Structure of Human Populations [PDF]
Y Chromosome Microsatellite Data
used by Pritchard et al (1999) MBE. Population growth of human Y chromosomes: a study of Y chromosome microsatellites [PDF]
Plots of linkage disequilibrium for several early human data sets.
These are expanded versions of figures found in a review by Wall and Pritchard
(2003) [August issue of Nature Reviews Genetics].
Additional recombination rate estimates for Conrad et al. (2006) A worldwide survey of haplotype variation and linkage disequilibrium in the human genome. Nature Genetics