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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
SEMG2 ENST00000372769 98.84 81.58 92.95 0.10 0.33 0.14 0.11 0.52 0.15
ZNF321P ENST00000391777 98.83 92.13 97.95 0.10 0.24 0.09 0.11 0.32 0.04
BTN3A2 ENST00000356386 98.83 77.77 91.24 0.10 0.42 0.15 0.11 0.79 0.18
ARIH2OS ENST00000408959 98.82 99.81 99.95 0.10 0.17 0.13 0.11 0.11 0.04
C10orf111 ENST00000378207 98.82 99.50 99.93 0.10 0.16 0.12 0.11 0.13 0.04
LENG9 ENST00000333834 98.81 98.12 99.81 0.10 0.20 0.12 0.11 0.16 0.04
FTHL17 ENST00000359202 98.81 98.69 99.85 0.10 0.18 0.12 0.11 0.15 0.04
OR7G3 ENST00000305444 98.80 99.70 99.94 0.10 0.17 0.12 0.11 0.11 0.04
DPRX ENST00000376650 98.80 96.33 99.27 0.10 0.22 0.11 0.11 0.19 0.04
C3orf72 ENST00000383165 98.79 93.28 98.33 0.10 0.28 0.09 0.11 0.30 0.05
TREML4 ENST00000341495 98.79 87.44 95.85 0.10 0.23 0.07 0.11 0.40 0.11
LGALS16 ENST00000392051 98.78 87.88 96.07 0.10 0.24 0.07 0.11 0.38 0.11
PI3 ENST00000243924 98.78 84.17 94.23 0.10 0.27 0.10 0.11 0.44 0.12
MGARP ENST00000398955 98.77 93.22 98.31 0.10 0.28 0.09 0.11 0.30 0.05
LAIR2 ENST00000301202 98.77 92.15 97.94 0.10 0.25 0.09 0.11 0.32 0.04
LINC00696 ENST00000541313 98.76 97.58 99.58 0.10 0.22 0.12 0.11 0.20 0.05
MS4A14 ENST00000531783 98.76 87.83 96.01 0.10 0.24 0.07 0.11 0.38 0.11
CD300LB ENST00000392621 98.75 83.27 93.80 0.10 0.28 0.10 0.11 0.47 0.13
C3orf56 ENST00000398112 98.74 98.08 99.68 0.10 0.20 0.12 0.11 0.16 0.04
MRGPRX2 ENST00000329773 98.74 99.21 99.89 0.10 0.15 0.12 0.11 0.13 0.04
WFDC11 ENST00000356562 98.73 86.59 95.42 0.10 0.24 0.08 0.11 0.40 0.11
ZNF582 ENST00000301310 98.73 86.78 95.51 0.10 0.24 0.08 0.11 0.40 0.11
SEMG1 ENST00000372781 98.72 73.65 89.29 0.10 0.52 0.19 0.11 1.03 0.25
KLK2 ENST00000325321 98.72 75.69 90.25 0.10 0.44 0.16 0.11 0.89 0.22
ULBP1 ENST00000229708 98.71 80.18 92.11 0.10 0.37 0.14 0.11 0.59 0.16

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