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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
DRD4 ENST00000176183 85.56 93.12 92.05 0.28 0.28 0.14 0.46 0.30 0.16
PTPN18 ENST00000175756 74.56 51.66 64.38 0.38 0.62 0.51 0.79 1.87 1.34
ASNS ENST00000175506 31.68 40.25 34.22 0.95 0.61 0.87 1.70 1.73 1.77
ADAM7 ENST00000175238 76.06 56.05 67.98 0.34 0.49 0.51 0.78 1.55 1.10
LAPTM4A ENST00000175091 52.50 47.63 48.95 0.65 0.62 0.71 1.80 1.97 1.84
MNT ENST00000174618 39.01 3.87 19.44 0.90 3.30 1.53 1.76 0.31 0.84
TRO ENST00000173898 79.58 43.83 62.63 0.33 0.61 0.48 0.58 1.95 1.40
ISOC1 ENST00000173527 57.77 76.09 68.98 0.57 0.43 0.46 1.55 0.86 1.04
NTN1 ENST00000173229 32.37 2.58 15.24 0.99 3.54 1.83 1.70 0.29 0.65
NGFR ENST00000172229 38.30 27.72 31.23 0.91 1.27 0.86 1.73 1.18 1.56
TNS1 ENST00000171887 37.77 16.61 25.27 0.92 1.75 1.05 1.73 0.71 1.15
P2RY10 ENST00000171757 24.01 57.07 38.86 1.35 0.56 0.80 1.10 1.51 2.05
KEAP1 ENST00000171111 8.05 32.36 18.16 2.58 0.87 1.66 0.43 1.46 0.79
GPATCH1 ENST00000170564 47.86 34.62 39.59 0.52 0.80 0.80 1.80 1.54 2.04
MKRN2 ENST00000170447 51.58 36.79 42.44 0.59 0.76 0.68 1.85 1.65 2.01
REXO1 ENST00000170168 79.51 12.69 44.66 0.34 2.10 0.62 0.57 0.58 2.06
BPIFB2 ENST00000170150 71.73 67.12 72.03 0.35 0.54 0.43 0.81 1.22 0.81
TIMM21 ENST00000169551 71.12 61.80 68.45 0.42 0.57 0.47 0.85 1.37 1.06
ST6GAL1 ENST00000169298 18.76 29.35 22.20 1.56 1.10 1.15 0.91 1.36 0.96
NMRK2 ENST00000168977 86.71 94.88 93.53 0.24 0.23 0.13 0.40 0.23 0.15
FGF4 ENST00000168712 56.04 60.46 58.30 0.58 0.52 0.48 1.62 1.41 1.65
HSD17B10 ENST00000168216 0.58 19.28 7.28 4.38 1.47 2.80 0.19 0.76 0.34
SPP2 ENST00000168148 84.16 92.91 91.44 0.32 0.29 0.15 0.48 0.30 0.18
KRT20 ENST00000167588 72.80 70.29 74.47 0.32 0.52 0.40 0.79 1.10 0.69
KRT14 ENST00000167586 29.00 45.02 35.18 1.10 0.68 0.86 1.54 1.96 1.75

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