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Table 1 Sets of genes used in analysis

From: Exome-wide search and functional annotation of genes associated in patients with severe tick-borne encephalitis in a Russian population

Gene set Description Number of genes / proteins
Cases Genes harboring pathogenic variants found in exomes of patients with TBE, that were not common in non-Finnish Europeans (MAF < 0.05) 4509
Control Genes harboring pathogenic variants found in exomes of individuals from the control cohort, that were not common in non-Finnish Europeans (MAF < 0.05) 3684
Cases_only Genes harboring rare pathogenic variants in exomes of patients with TBE only and not containing any rare pathogenic variants in exomes of individuals from the control cohort. 2407
ECM proteoglycans - cell periphery set Genes from the cases_only set that, according to DAVID tool, are annotated by at least one of the following four enriched GO terms: (1) cell periphery; (2) plasma membrane; (3) plasma membrane part; (4) integral component of plasma membrane; or belonging to ECM proteoglycans pathway 749
TBEVHostDB Genes that are probably involved in response to TBEV infection (http://icg.nsc.ru/TBEVHostDB/) 140
Associated Genes harboring genetic variants associated with severe forms of TBE at P-value < 0.01. The search of associated variants was performed based on whole-exome sequencing of 22 patients with TBE and 17 control individuals with PLINK software. 667
Associated_possibly damaging Genes from the associated set that harbored only potentially damaging genetic variants. The following types of variants were considered to be potentially damaging: all nonsynonymous, frameshift and stopgain variants, as well as variants annotated by PolyPhen2 or SIFT databases as probably damaging or possibly damaging. 132
Associated_harmful Genes from the associated set that harbored harmful genetic variants. The following types of variants were considered to be harmful: (1) variants annotated by PolyPhen2 or SIFT databases as probably damaging or possibly damaging, as well as (2) one additional stopgain variant. 46