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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
ACTBL2 ENST00000423391 61.63 96.26 82.31 0.68 0.22 0.33 1.29 0.19 0.44
ACTC1 ENST00000290378 0.24 22.62 8.78 4.50 1.47 2.49 0.16 0.86 0.37
ACTG1 ENST00000575842 1.57 46.66 22.26 4.26 0.75 1.16 0.20 1.97 0.96
ACTG2 ENST00000409624 4.51 32.60 16.36 3.70 0.86 1.71 0.29 1.47 0.67
ACTL10 ENST00000330271 86.60 75.42 84.33 0.24 0.46 0.33 0.41 0.90 0.41
ACTL6A ENST00000429709 2.31 8.48 2.82 4.12 2.52 4.03 0.28 0.46 0.23
ACTL6B ENST00000160382 2.50 34.20 16.15 4.08 0.84 1.71 0.27 1.55 0.66
ACTL7A ENST00000333999 60.26 75.51 70.10 0.61 0.44 0.46 1.39 0.90 0.90
ACTL7B ENST00000374667 68.17 81.92 78.30 0.56 0.35 0.38 1.02 0.51 0.54
ACTL8 ENST00000375406 81.99 65.96 77.14 0.30 0.56 0.35 0.57 1.23 0.59
ACTL9 ENST00000324436 77.55 61.62 72.24 0.34 0.54 0.43 0.69 1.40 0.82
ACTN1 ENST00000394419 11.31 6.94 6.46 1.76 2.58 3.07 0.59 0.37 0.32
ACTN2 ENST00000366578 20.08 8.13 11.73 1.53 2.53 2.21 1.01 0.44 0.47
ACTN4 ENST00000252699 6.48 1.05 1.66 3.04 4.06 4.26 0.37 0.28 0.23
ACTR10 ENST00000254286 31.53 35.23 31.59 0.95 0.76 0.89 1.69 1.58 1.58
ACTR1A ENST00000369905 3.36 14.59 6.25 3.85 2.04 3.14 0.30 0.61 0.32
ACTR1B ENST00000289228 53.62 36.22 43.29 0.62 0.82 0.63 1.77 1.61 2.01
ACTR2 ENST00000377982 1.02 5.68 1.38 4.37 2.96 4.36 0.18 0.34 0.23
ACTR3 ENST00000263238 2.71 1.75 0.72 4.02 3.83 4.60 0.29 0.26 0.20
ACTR3B ENST00000256001 15.00 5.58 7.65 1.56 2.99 2.71 0.75 0.33 0.33
ACTR3C ENST00000539352 84.21 76.10 83.51 0.30 0.43 0.33 0.47 0.86 0.40
ACTR5 ENST00000243903 53.30 55.03 53.62 0.62 0.57 0.63 1.74 1.63 1.82
ACTR6 ENST00000188312 13.58 59.02 34.52 1.66 0.51 0.90 0.67 1.43 1.77
ACTR8 ENST00000335754 38.27 55.86 45.76 0.92 0.51 0.68 1.73 1.57 1.97
ACTRT1 ENST00000371124 83.38 82.45 86.15 0.30 0.34 0.33 0.52 0.52 0.33

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