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The correct estimation of standard errors with PIAAC data is done with the Stata command, repest (see Stata help for more details).

While the GIRO Web Portal solves a number of everyday tasks that require knowledge of the latest ionograms around the world, expert-level processing and visualization of the data is done with the SAO Explorer and Drift Explorer software applications connected to the GIRO databases.

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Analysis of raw data was done with the BIO-PLEX manager software (Version 4.1, BioRad Laboratories, Hercules, CA, USA).

Analysis of the acquired resting-state data was done with the two-stage Ncut group clustering approach and the resulting group RSNs are discussed on their functional relevance, overlap and differences with previous reported resting-state studies.

Directed content analysis of qualitative data was done with the help of NVIVO v10.0.

All data were done with the Statistical Package for Social Sciences SPSSS 17.0 for windows).

Analysis of sequencing data was done with the GATK v2 package as per the recommendations of the Broad Institute [ 41].

The quality control, summarization and normalization of ncRNA expression data was done with the miRNA QC Tool v.1.0.33.0 software by Affymetrix.

The analysis of microarray data was done with the R statistical package version 2.15.0 [ 37] and Bioconductor libraries version 1.4.7 [ 38].

All ANN calculations were performed using a C++ program (written by the authors and available upon request) while pre-processing of the data was done with the publicly available statistical software R [ 25].

Meta-analysis of all the available data was done, with the combined analysis showing no significant role for rs17388568 in the development of RA (OR = 1.03, (0.98 to 1.09), P = 0.22).

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