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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
C10orf115 ENST00000376501 90.52 92.22 94.30 0.16 0.25 0.10 0.24 0.31 0.12
RPS4Y2 ENST00000288666 90.53 95.61 96.80 0.16 0.23 0.08 0.24 0.21 0.07
FAM228B ENST00000420135 90.53 73.76 85.65 0.16 0.52 0.32 0.24 1.03 0.34
RP11-65D24.2 ENST00000375713 90.54 73.56 85.58 0.16 0.52 0.32 0.24 1.03 0.35
FLJ20373 ENST00000414004 90.54 98.00 97.21 0.16 0.20 0.08 0.24 0.17 0.06
SOWAHD ENST00000343905 90.55 70.55 83.86 0.16 0.52 0.35 0.24 1.08 0.42
GOLGA8Q ENST00000562783 90.55 85.28 91.04 0.16 0.25 0.15 0.24 0.46 0.20
SPANXC ENST00000358993 90.56 95.23 95.81 0.16 0.23 0.07 0.24 0.21 0.11
COX6A2 ENST00000287490 90.56 82.87 89.98 0.16 0.32 0.18 0.24 0.49 0.23
AL139099.1 ENST00000539688 90.57 98.01 97.12 0.16 0.20 0.08 0.24 0.16 0.07
NPIPB3 ENST00000458643 90.57 91.98 95.07 0.16 0.23 0.09 0.24 0.33 0.10
POTEB2 ENST00000454856 90.58 88.36 93.08 0.16 0.23 0.14 0.24 0.37 0.15
RP11-1105G2.3 ENST00000551941 90.58 92.49 94.46 0.16 0.28 0.10 0.24 0.30 0.12
AC007390.5 ENST00000402297 90.59 88.77 92.61 0.16 0.25 0.14 0.24 0.36 0.15
KIAA1731 ENST00000325212 90.59 24.57 57.77 0.16 1.30 0.49 0.24 1.05 1.67
TWIST2 ENST00000448943 90.60 64.28 81.90 0.16 0.49 0.37 0.24 1.20 0.46
AC135178.1 ENST00000535173 90.60 98.01 97.24 0.16 0.20 0.08 0.24 0.16 0.07
C5orf27 ENST00000357880 90.61 94.89 95.69 0.16 0.23 0.07 0.24 0.23 0.11
ZNF865 ENST00000568956 90.62 3.81 46.09 0.16 3.30 0.68 0.24 0.31 1.97
CASP16 ENST00000428155 90.62 77.08 87.21 0.16 0.42 0.28 0.24 0.78 0.31
SMKR1 ENST00000462322 90.63 83.37 90.23 0.16 0.27 0.16 0.24 0.48 0.21
ADO ENST00000373783 90.63 43.74 69.54 0.16 0.62 0.44 0.24 1.95 0.96
AL355149.2 ENST00000601199 90.64 98.03 97.27 0.16 0.20 0.08 0.24 0.16 0.07
AC110619.2 ENST00000404327 90.64 78.57 88.06 0.16 0.40 0.23 0.24 0.74 0.30
AC145676.2 ENST00000514988 90.65 98.04 97.28 0.16 0.20 0.08 0.24 0.16 0.07

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