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Plain Text icon README_Raj_et_al_2013.txt — Plain Text, 2 KB (3042 bytes)

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The present readme file refer to the full results (available in this webpage) of the manuscript entitled:
Raj, S.M., Pagani, L., Gallego Romero, I., Kivisild, T. & Amos, W. 2013.
"A general linear model-based approach for inferring selection to climate."
BMC Genetics 

In that file, each of the reported 28784 genic windows was analysed for each of the 8 climate variables for each of 2 tests of significance through different methods of randomization, giving a total of 460544 independent results.

The column headers of the table are:

"Info on Genic Region"
RegionNumber: any given genic windows showing statistical significance is often flanked by one or many adjacent windows that also show significant associations, either through linkage disequilibrium or presence of related genes.  Such groups are combined into independent genic regions, numbered consecutively from 0Mb on chromosome 1.  Each number represents a unique combination of consecutive genic windows+climate variable+randomization method.
RegionClass: the p-value range of the genic region
Top_p_value_in_region: the highest p-value observed in the region
How_many_p<=10-5: how many "hits", defined as P<=10-5 are observed in the region

"Info on Genic Window"
WindowNumber: the number of the genic window.  These are numbered consecutively in the master list of genes but some could not be included due to the low density of SNPs genotyped in the relevant region in our dataset.
Chr: chromosome of the genic window
MidPoint: midpoint of the genic window
p-value: worldwide p-value for that window under a specific climate variable and randomization condition
Does_it_match_region_top_p?: 0 if this is not the top window in the region, 1 if this is the top window in the region
ENSEMBL_GENE: Ensembl ID of the gene included in that region
HUGO_GENE: Hugo name (if available)

"Info on Climate Variable"
Climate: Climate variable considered for this genic window. Sr (Solar Radiation), Pr (Precipitable Water), rH (relative humidity), T (Temperature).
Season: Winter (October to March for the Northern Hemisphere) or Summer (April to September for the Northern Emisphere). For the Southern Hemisphere the seasons where swopped.
ContinentScrambling: 1 if the randomization was performed only within each continent, the more conservative approach where associations arising purely through climate differences between continents are eliminated, 0 if the randomization was performed worldwide
Europe and Altai p-value: p-value obtained for the European and Altaian populations alone
Middle East and North Africa: region-specific P-value as above
Central and South Asia: region-specific P-value as above
East Asia: region-specific P-value as above
Oceania: region-specific P-value as above
Native Americans: region-specific P-value as above

These data are freely available but if you intend to use these results for meta analyses or to expand the results of other analyses, we ask you please to cite our work.