Table 1 Sets of genes used in analysis
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 |