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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
RPS18 ENST00000439602 0.39 9.45 2.51 4.39 2.48 4.01 0.16 0.49 0.24
GNAQ ENST00000286548 0.40 7.47 1.81 4.39 2.54 4.22 0.16 0.40 0.23
UBE2E3 ENST00000410062 0.40 33.66 14.81 4.38 0.84 1.95 0.16 1.55 0.62
CSNK1A1 ENST00000515768 0.41 6.67 1.54 4.38 2.67 4.31 0.18 0.37 0.22
SF3B4 ENST00000271628 0.41 6.61 1.52 4.37 2.64 4.33 0.17 0.37 0.22
SRSF7 ENST00000313117 0.42 12.03 3.62 4.37 2.06 3.85 0.17 0.57 0.23
ZEB2 ENST00000558170 0.42 1.34 0.11 4.36 3.97 4.88 0.17 0.27 0.17
KCNC1 ENST00000265969 0.43 9.93 2.68 4.38 2.32 4.01 0.17 0.50 0.23
SMC1A ENST00000322213 0.43 0.28 0.02 4.38 4.12 4.90 0.17 0.29 0.15
ARL8A ENST00000272217 0.44 16.84 5.90 4.40 1.66 3.30 0.17 0.71 0.29
SIAH1 ENST00000356721 0.44 24.04 9.75 4.39 1.38 2.26 0.17 0.96 0.40
HMGA1 ENST00000447654 0.45 26.14 10.92 4.39 1.19 2.21 0.17 1.08 0.44
PCBP2 ENST00000359462 0.45 7.90 1.96 4.39 2.53 4.13 0.17 0.44 0.24
PSMC2 ENST00000435765 0.46 1.66 0.18 4.38 3.84 4.89 0.17 0.26 0.18
KCTD9 ENST00000221200 0.46 23.38 9.38 4.38 1.40 2.29 0.17 0.93 0.39
ZMAT2 ENST00000274712 0.47 9.30 2.48 4.40 2.48 4.03 0.17 0.47 0.24
NKAP ENST00000371410 0.48 4.04 0.75 4.39 3.25 4.58 0.17 0.32 0.20
TUBB4B ENST00000340384 0.48 20.61 7.88 4.41 1.46 2.63 0.17 0.76 0.35
TRA2B ENST00000453386 0.49 8.63 2.22 4.41 2.49 4.07 0.18 0.47 0.23
GRIN2B ENST00000609686 0.49 0.23 0.02 4.40 4.11 4.89 0.18 0.28 0.15
SPIN1 ENST00000375859 0.50 10.83 3.11 4.40 2.14 3.93 0.18 0.50 0.24
AP2M1 ENST00000292807 0.50 5.23 1.07 4.40 3.15 4.42 0.18 0.32 0.21
KCNB1 ENST00000371741 0.51 2.33 0.31 4.39 3.63 4.84 0.18 0.29 0.18
SMC3 ENST00000361804 0.51 0.03 0.01 4.39 4.10 4.90 0.19 0.26 0.15
RBPJ ENST00000342295 0.52 5.76 1.24 4.38 2.88 4.40 0.19 0.34 0.21

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