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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
MECOM ENST00000264674 5.43 2.44 1.80 3.34 3.59 4.22 0.32 0.29 0.23
RAB39B ENST00000369454 5.43 26.40 13.55 3.33 1.18 2.05 0.32 1.09 0.57
IRF6 ENST00000367021 5.44 2.31 1.75 3.31 3.63 4.22 0.33 0.29 0.23
ELAVL2 ENST00000397312 5.44 6.15 3.25 3.31 2.75 3.88 0.33 0.35 0.24
TYMS ENST00000323274 5.45 21.05 10.86 3.31 1.44 2.19 0.33 0.83 0.44
CACNA1I ENST00000402142 5.45 5.38 2.87 3.31 3.05 4.01 0.33 0.32 0.23
RLF ENST00000372771 5.46 0.04 1.02 3.31 4.09 4.46 0.33 0.28 0.21
PCMTD1 ENST00000360540 5.46 28.17 14.53 3.31 1.18 2.00 0.33 1.21 0.59
GATA3 ENST00000379328 5.47 18.18 9.26 3.31 1.49 2.32 0.33 0.75 0.38
MBNL2 ENST00000345429 5.47 28.66 14.82 3.31 1.18 1.95 0.33 1.29 0.62
TUBA4A ENST00000248437 5.48 32.62 16.89 3.33 0.85 1.68 0.33 1.47 0.70
OSTM1 ENST00000193322 5.49 33.76 17.48 3.33 0.85 1.62 0.33 1.56 0.75
SSU72 ENST00000291386 5.49 26.57 13.69 3.31 1.19 2.04 0.33 1.12 0.58
RAP2C ENST00000342983 5.50 65.53 33.68 3.31 0.53 0.90 0.33 1.22 1.73
PDZD11 ENST00000239666 5.50 49.35 25.52 3.30 0.65 1.05 0.33 2.01 1.19
ISL1 ENST00000230658 5.51 18.13 9.27 3.30 1.53 2.32 0.33 0.74 0.38
COX6B1 ENST00000246554 5.51 63.89 32.88 3.30 0.48 0.86 0.33 1.22 1.67
DUSP7 ENST00000495880 5.52 26.24 13.49 3.29 1.19 2.05 0.33 1.08 0.57
KIF3A ENST00000378746 5.52 12.98 6.64 3.28 2.07 3.01 0.33 0.59 0.32
PRKG1 ENST00000373980 5.53 5.74 3.07 3.26 2.90 3.94 0.33 0.34 0.23
DDB1 ENST00000301764 5.53 7.15 3.71 3.26 2.58 3.81 0.33 0.37 0.23
TMED2 ENST00000262225 5.54 19.40 10.04 3.26 1.46 2.26 0.33 0.74 0.42
ERP44 ENST00000262455 5.54 10.66 5.40 3.26 2.14 3.48 0.33 0.51 0.25
TCF7L2 ENST00000543371 5.55 10.77 5.50 3.26 2.11 3.43 0.33 0.51 0.26
GPBP1 ENST00000264779 5.55 18.63 9.55 3.25 1.49 2.29 0.33 0.75 0.40

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