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Genes Fold Enrichment Color Codes
  • Gene Name, Canonical Transcript - gene identifiers from gnomAD database (Build 37)
  • GeVIR % - gene rank measured in percentiles based on Gene Variation Intolerance Ranking (GeVIR) (low values indicate more variation intolerant genes, which is also true for "LOEUF %" and "VIRLoF %"). GeVIR is a method which we developed and applied on a list of 19,361 genes to sort them based on number, length and evolutionary conservation of regions without functional variants (i.e. between two missense, loss-of-function, insertion or delition variants) in gnomAD database (version 2.0.1). Only canonical transcripts were analysed.
  • LOEUF % - gene rank measured in percentiles based gnomAD loss-of-function observed/expected upper bound fraction (LOEUF) (see Figure 1). For more information about this metric, please read "Constraint" section of MacArthur Lab blog post. If you use this metric please cite gnomAD flagship paper and use most up-to-date values from gnomAD website.

    LoF observed/expected (o/e) upper Confidence Interval (CI)

    Figure 1. Screenshot of ELN gene constraint metrics from gnomAD browser

  • VIRLoF % - gene rank measured in percentiles based on both GeVIR and gnomAD LOEUF (shows the best overall performance, see Figure 2). If you use this metric please cite both GeVIR and gnomAD flagship paper.
  • GeVIR AD, LOEUF AD, VIRLoF AD, GeVIR AR, LOEUF AR, VIRLoF AR - to help users interpret gene ranks, we calculated fold enrichment of Autosomal Dominant (AD) and Autosomal Recessive (AR) genes with known molecular basis of disorder in OMIM in a range of +-5% of gene X (see Figure 2). Statistical significant fold enrichements (Fisher Exact Test p-value < 1e-5) are shown in bold in the table. For example CDK19 gene's GeVIR % is 2.37, so examined range is from 0 (2.37-5, rounded to minimal percentile) to 7.37% (2.37+5). Genes in this range are ~4 times more often (4.05 fold enrichement) associated with AD diseases and ~4 times less often (0.25 fold enrichement) associated with AR diseases. Both enrichment of AD genes and deficiency of AR genes is statistical significant. Thus GeVIR metric adds supportive evidence that CDK19 is more likely to be associated with AD than AR disease.

    Gene Percentiles AD AR Fold Enrichment

    Figure 2. Fold Enrichment of known Autosomal Dominant (AD) and Autosomal Recessive (AR) genes of each gene in the ranked lists (GeVIR, LOEUF, VIRLoF. AD genes are enriched among top ranked genes (lowest percentiles), whereas AR genes are enriched among middle ranked genes (approximetly 35-65 percentiles). Combined metric (VIRLoF, purple) shows the best perfornance, i.e. high ranked genes are more often associated with AD than AR diseases, low ranked genes are less often associated with both AD and AR diseases.
Gene Name Canonical Transcript GeVIR % LOEUF % VIRLoF % GeVIR AD LOEUF AD VIRLoF AD GeVIR AR LOEUF AR VIRLoF AR
TRRAP ENST00000359863 4.00 0.26 0.65 3.77 4.11 4.64 0.29 0.28 0.20
ATP1A3 ENST00000545399 0.88 0.27 0.04 4.35 4.11 4.87 0.18 0.29 0.15
GIGYF2 ENST00000409451 10.81 0.27 2.96 1.94 4.10 3.99 0.57 0.29 0.23
SMC1A ENST00000322213 0.43 0.28 0.02 4.38 4.12 4.90 0.17 0.29 0.15
SUPT6H ENST00000314616 4.37 0.28 0.78 3.71 4.12 4.56 0.30 0.29 0.21
ANKRD17 ENST00000358602 2.31 0.29 0.27 4.12 4.12 4.83 0.28 0.29 0.18
DYNC1H1 ENST00000360184 1.82 0.29 0.19 4.29 4.11 4.88 0.22 0.29 0.18
HCFC1 ENST00000310441 7.37 0.30 1.73 2.86 4.11 4.23 0.39 0.29 0.23
NPEPPS ENST00000322157 6.32 0.30 1.33 3.04 4.13 4.34 0.35 0.29 0.23
USP7 ENST00000344836 1.74 0.31 0.15 4.30 4.12 4.84 0.22 0.29 0.18
CHERP ENST00000546361 8.94 0.32 2.31 2.35 4.14 4.03 0.45 0.28 0.22
RRM1 ENST00000300738 5.05 0.32 0.98 3.52 4.14 4.44 0.30 0.28 0.21
RPRD2 ENST00000369068 13.92 0.33 4.39 1.59 4.14 3.72 0.71 0.28 0.24
UBR5 ENST00000520539 4.52 0.33 0.82 3.69 4.13 4.55 0.29 0.28 0.21
CREBBP ENST00000262367 6.74 0.34 1.54 2.99 4.15 4.32 0.37 0.28 0.22
WDFY3 ENST00000295888 6.25 0.34 1.33 3.04 4.15 4.34 0.35 0.28 0.22
KMT2A ENST00000534358 5.67 0.35 1.18 3.19 4.14 4.43 0.33 0.28 0.21
CHD7 ENST00000423902 7.71 0.35 1.87 2.73 4.14 4.18 0.40 0.28 0.24
SF3B1 ENST00000335508 0.06 0.36 0.01 4.58 4.14 4.91 0.15 0.28 0.15
PRPF3 ENST00000324862 2.82 0.36 0.41 3.97 4.13 4.78 0.28 0.28 0.18
ZSWIM6 ENST00000252744 18.93 0.37 7.00 1.58 4.13 2.88 0.94 0.28 0.33
PPFIA1 ENST00000253925 26.60 0.37 11.13 1.33 4.12 2.19 1.31 0.28 0.45
EIF3B ENST00000360876 16.34 0.38 5.65 1.48 4.12 3.37 0.81 0.28 0.27
KAT6A ENST00000396930 14.53 0.38 4.77 1.54 4.14 3.67 0.73 0.28 0.25
GLTSCR1L ENST00000314073 10.20 0.39 2.75 2.02 4.14 4.03 0.54 0.28 0.23

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