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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
ERVV-2 ENST00000601417 90.44 97.94 97.44 0.15 0.20 0.08 0.25 0.17 0.07
ANKDD1B ENST00000601380 90.39 58.54 77.81 0.15 0.54 0.38 0.25 1.40 0.54
ZNF558 ENST00000601372 46.05 61.22 53.04 0.58 0.53 0.61 1.80 1.40 1.87
MYH14 ENST00000601313 20.43 11.96 13.88 1.53 2.07 2.10 1.03 0.59 0.59
ARL14EPL ENST00000601302 88.16 68.78 81.83 0.20 0.53 0.37 0.35 1.19 0.47
IRF3 ENST00000601291 65.51 48.24 56.68 0.57 0.63 0.52 1.09 2.00 1.71
SCGB2B2 ENST00000601241 82.54 92.99 90.83 0.30 0.28 0.15 0.56 0.30 0.20
AL355149.2 ENST00000601199 90.64 98.03 97.27 0.16 0.20 0.08 0.24 0.16 0.07
CXCL17 ENST00000601181 48.99 78.61 65.25 0.54 0.40 0.53 1.80 0.74 1.31
SEPW1 ENST00000601048 74.86 75.77 78.55 0.38 0.43 0.38 0.78 0.88 0.55
CKS1B ENST00000600888 91.28 98.34 97.72 0.15 0.21 0.09 0.20 0.14 0.05
IL12RB1 ENST00000600835 95.23 49.38 75.21 0.10 0.65 0.37 0.11 2.01 0.67
AC079210.1 ENST00000600820 75.17 99.68 90.08 0.38 0.17 0.18 0.76 0.12 0.22
RPS28 ENST00000600659 3.34 42.32 20.94 3.85 0.61 1.43 0.29 1.90 0.87
AP000889.3 ENST00000600612 79.78 86.94 86.56 0.33 0.22 0.30 0.58 0.40 0.33
ITFG3 ENST00000600536 81.93 65.59 76.90 0.32 0.53 0.35 0.57 1.22 0.60
TMEM59L ENST00000600490 60.22 47.49 53.28 0.61 0.62 0.61 1.40 2.01 1.86
AC087645.1 ENST00000600484 76.88 54.05 67.30 0.34 0.65 0.52 0.73 1.69 1.15
EPB41L4A-AS2 ENST00000600409 92.37 98.94 98.27 0.15 0.17 0.09 0.18 0.15 0.05
ZSCAN18 ENST00000600404 45.11 35.66 38.65 0.63 0.78 0.82 1.75 1.57 2.01
STAP2 ENST00000600324 78.10 77.49 81.14 0.34 0.42 0.39 0.67 0.78 0.49
ZNF574 ENST00000600245 30.55 24.50 25.62 0.99 1.32 1.06 1.63 1.01 1.20
ZNF616 ENST00000600228 97.60 90.31 96.75 0.10 0.25 0.08 0.11 0.38 0.08
MTRNR2L12 ENST00000600213 92.23 98.85 97.10 0.15 0.16 0.08 0.18 0.14 0.07
CTB-167G5.5 ENST00000600193 93.66 86.59 92.93 0.13 0.24 0.14 0.13 0.40 0.15

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