Computational protocol: Gene-Gene Interaction and Functional Impact of Polymorphisms on Innate Immune Genes in Controlling Plasmodium falciparum Blood Infection Level

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Protocol publication

[…] The allele and genotype frequencies for IL12B SNPs were estimated by gene counting and Hardy–Weinberg equilibrium was evaluated by χ2 test using Haploview (http://www.broad.mit.edu/mpg/haploview/). Pairwise comparisons between log-transformed parasitemia and genotypic classes for IL12Bpro and +1188 loci were analyzed by model based independent t test and ANOVA F-ratio. The results were further validated using non-parametric Wilcoxon Rank sum and Kruskal Wallis H tests. Bonferroni correction was done for multiple testing. For allele based risk assessment, the unprocessed parasitemia data was previously dichotomized into high (N = 88) and low (N = 205) parasitemic groups employing the two component mixture model and expectation-maximization algorithm and a threshold value of 7520 parasites/µl or 3.88 log-parasitemia was derived as the cutoff. Detailed procedure of this strategy was described earlier . The proportion of the risk allele for each locus was compared between high and low parasitemic groups using a two-way contingency table. [...] To find out the potential microRNA binding sites within IL12B mRNA, the entire IL12B 3′UTR region was scanned using miRNA-target prediction databases such as TargetScan (www.targetscan.org/), miRBase (www.mirbase.org/), microRNA.org (www.microrna.org/), RegRNA (www.regrna.mbc.nctu.edu.tw/), MicroCosm (www.ebi.ac.uk/enright-srv/microcosm/). Target microRNAs were selected and compiled on the basis of its conserved seed match or a seed match with a higher context score. The thermodynamic stability of the mRNA-miRNA duplex was calculated using RNAHybrid (www.bibiserv.techfak.uni-bielefeld.de/rnahybrid/). […]

Pipeline specifications

Software tools Haploview, TargetScan, RegRNA, RNAhybrid
Databases microRNA.org miRBase
Applications Transcription analysis, GWAS
Organisms Plasmodium falciparum, Homo sapiens
Diseases Malaria, Malaria, Falciparum
Chemicals Dactinomycin