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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
FAM193A ENST00000324666 30.35 7.03 16.53 1.02 2.57 1.71 1.60 0.37 0.69
LIN7A ENST00000552864 30.35 75.61 52.22 1.02 0.44 0.61 1.60 0.91 1.90
ATF6 ENST00000367942 30.36 36.55 31.66 1.02 0.78 0.89 1.60 1.63 1.58
ISM1 ENST00000262487 30.37 34.66 30.78 1.02 0.80 0.77 1.60 1.54 1.49
RGS2 ENST00000235382 30.37 75.32 52.08 1.02 0.49 0.61 1.60 0.90 1.92
NRP2 ENST00000360409 30.38 23.84 25.18 1.02 1.38 1.05 1.60 0.93 1.16
RAB33B ENST00000305626 30.38 30.74 28.70 1.02 1.06 0.80 1.60 1.36 1.34
C1QTNF3 ENST00000382065 30.39 71.33 49.83 1.02 0.53 0.65 1.60 1.06 1.90
STRN ENST00000263918 30.39 16.40 21.52 1.01 1.81 1.30 1.60 0.69 0.91
WDR83OS ENST00000596731 30.40 84.86 57.58 1.01 0.27 0.51 1.60 0.43 1.67
MAD2L1 ENST00000296509 30.40 50.52 38.72 1.01 0.63 0.82 1.60 1.95 2.02
MINOS1 ENST00000322753 30.41 29.37 28.08 1.00 1.10 0.81 1.60 1.36 1.29
TECTA ENST00000392793 30.41 29.77 28.26 1.00 1.13 0.80 1.60 1.40 1.29
ZC4H2 ENST00000374839 30.42 17.90 22.32 1.00 1.53 1.16 1.60 0.73 0.97
DPY19L3 ENST00000342179 30.42 32.41 29.58 1.00 0.87 0.84 1.60 1.48 1.39
TSPAN31 ENST00000257910 30.43 36.67 31.78 1.00 0.77 0.89 1.61 1.66 1.58
SH3RF1 ENST00000284637 30.43 27.90 27.30 1.00 1.20 0.97 1.61 1.19 1.24
TTC5 ENST00000258821 30.44 42.33 34.58 1.00 0.61 0.90 1.61 1.90 1.77
ANKRD54 ENST00000215941 30.44 43.90 35.39 1.00 0.61 0.87 1.61 1.96 1.77
DBNL ENST00000468694 30.45 26.06 26.35 1.00 1.20 1.00 1.61 1.10 1.26
ERBB3 ENST00000267101 30.45 35.41 31.11 1.00 0.77 0.84 1.61 1.56 1.53
TK1 ENST00000301634 30.46 41.09 33.94 1.00 0.59 0.90 1.61 1.81 1.73
BRD7 ENST00000394689 30.46 9.67 17.98 1.00 2.45 1.70 1.61 0.50 0.78
STX16 ENST00000371141 30.47 23.62 25.11 1.00 1.39 1.05 1.61 0.93 1.16
TFIP11 ENST00000407690 30.47 44.03 35.46 1.00 0.61 0.87 1.61 1.97 1.77

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