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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
OR1E2 ENST00000248384 73.48 76.48 78.24 0.34 0.42 0.37 0.79 0.84 0.55
SMIM8 ENST00000392863 73.48 93.23 86.54 0.34 0.28 0.30 0.79 0.30 0.33
ROPN1B ENST00000514116 73.49 78.11 79.12 0.34 0.43 0.39 0.78 0.74 0.54
MIEF2 ENST00000395706 73.49 45.86 60.10 0.34 0.75 0.48 0.78 2.01 1.61
CXCR3 ENST00000373691 73.50 55.21 65.99 0.34 0.57 0.51 0.78 1.62 1.23
UBQLNL ENST00000380184 73.50 84.15 82.20 0.34 0.27 0.35 0.78 0.45 0.45
FGA ENST00000302053 73.51 54.98 65.86 0.34 0.57 0.51 0.78 1.63 1.25
KDM8 ENST00000441782 73.51 45.94 60.16 0.34 0.76 0.48 0.78 2.02 1.61
MS4A2 ENST00000278888 73.52 85.87 83.06 0.34 0.28 0.30 0.78 0.43 0.40
FAM89B ENST00000530349 73.52 84.55 82.42 0.34 0.29 0.33 0.78 0.42 0.44
POTEH ENST00000343518 73.53 83.53 81.91 0.34 0.27 0.37 0.78 0.47 0.46
CDCP2 ENST00000371330 73.53 88.57 84.36 0.34 0.24 0.33 0.78 0.35 0.40
PRSS27 ENST00000302641 73.54 63.90 71.19 0.34 0.48 0.44 0.78 1.22 0.86
SPIB ENST00000595883 73.54 9.00 39.63 0.34 2.44 0.78 0.78 0.47 2.04
GPR141 ENST00000447769 73.55 96.01 87.91 0.34 0.23 0.24 0.78 0.20 0.32
NTF4 ENST00000301411 73.56 86.16 83.21 0.34 0.27 0.29 0.79 0.42 0.40
ALKBH2 ENST00000429722 73.56 68.28 73.72 0.35 0.52 0.42 0.79 1.20 0.71
CBR1 ENST00000290349 73.57 79.39 79.79 0.35 0.38 0.38 0.79 0.67 0.52
CYP3A5 ENST00000222982 73.57 72.31 75.97 0.35 0.51 0.38 0.79 1.03 0.62
IL34 ENST00000429149 73.58 30.50 51.12 0.35 1.09 0.65 0.79 1.37 1.89
CCDC81 ENST00000445632 73.58 68.18 73.68 0.35 0.52 0.42 0.79 1.21 0.72
EFCAB13 ENST00000331493 73.59 73.90 76.88 0.35 0.53 0.35 0.79 1.02 0.60
OR4C5 ENST00000319813 73.59 79.14 79.65 0.35 0.39 0.38 0.79 0.69 0.53
NKAPL ENST00000343684 73.60 55.35 66.15 0.35 0.57 0.52 0.79 1.61 1.20
MICU2 ENST00000382374 73.60 78.95 79.54 0.35 0.40 0.38 0.79 0.69 0.52

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