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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
TMED7-TICAM2 ENST00000282382 36.94 42.75 38.12 0.91 0.62 0.86 1.75 1.92 2.04
SCAND3 ENST00000452236 36.94 34.88 34.09 0.91 0.76 0.91 1.75 1.55 1.74
GPR119 ENST00000276218 36.95 71.06 53.42 0.91 0.49 0.62 1.75 1.07 1.84
RHBDF1 ENST00000262316 36.95 51.53 42.49 0.91 0.63 0.68 1.75 1.87 2.00
PCLO ENST00000333891 36.96 2.00 17.34 0.91 3.73 1.63 1.75 0.28 0.75
ANXA4 ENST00000394295 36.96 57.59 45.97 0.91 0.57 0.70 1.75 1.48 1.97
DNTTIP2 ENST00000436063 36.97 51.35 42.41 0.91 0.63 0.68 1.75 1.90 2.01
PITPNM1 ENST00000356404 36.97 20.13 26.70 0.91 1.43 1.00 1.75 0.74 1.27
ALX4 ENST00000329255 36.98 27.87 30.67 0.91 1.23 0.80 1.75 1.19 1.48
TEAD2 ENST00000598810 36.98 43.12 38.35 0.91 0.61 0.85 1.76 1.90 2.04
SUSD3 ENST00000375472 36.99 70.46 53.15 0.91 0.52 0.61 1.75 1.08 1.87
HMCN1 ENST00000271588 36.99 22.50 27.90 0.91 1.51 0.85 1.75 0.84 1.29
NODAL ENST00000287139 37.00 12.57 22.94 0.92 2.10 1.19 1.75 0.58 0.98
SLC25A17 ENST00000435456 37.00 53.98 43.87 0.92 0.65 0.62 1.75 1.70 2.02
WDR46 ENST00000374617 37.01 52.21 42.94 0.92 0.62 0.67 1.75 1.84 2.00
NPPA ENST00000376480 37.01 86.56 62.72 0.92 0.24 0.49 1.75 0.41 1.39
HEATR1 ENST00000366582 37.02 2.41 17.57 0.92 3.61 1.63 1.75 0.29 0.76
RAB28 ENST00000330852 37.02 40.82 37.20 0.92 0.62 0.81 1.75 1.78 1.97
LPAR4 ENST00000435339 37.03 88.05 63.81 0.92 0.25 0.49 1.75 0.38 1.38
XKR7 ENST00000562532 37.03 17.25 25.22 0.92 1.61 1.05 1.75 0.75 1.16
EPHA2 ENST00000358432 37.04 28.84 31.12 0.92 1.15 0.84 1.75 1.29 1.53
MVP ENST00000357402 37.04 38.56 35.91 0.92 0.72 0.86 1.75 1.67 1.78
ZNF81 ENST00000376954 37.05 25.01 29.18 0.92 1.33 0.84 1.76 1.05 1.33
ZFAT ENST00000377838 37.05 31.18 32.31 0.92 1.01 0.90 1.76 1.36 1.61
TNFAIP8L2 ENST00000368910 37.06 88.01 63.79 0.92 0.25 0.49 1.76 0.38 1.38

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