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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
FOXP4 ENST00000373060 11.76 7.59 7.02 1.66 2.51 2.90 0.59 0.42 0.33
LTA4H ENST00000228740 11.76 38.59 23.25 1.66 0.72 1.19 0.59 1.67 1.01
BOD1 ENST00000311086 11.77 50.64 29.38 1.66 0.63 0.84 0.59 1.95 1.36
TRAF7 ENST00000326181 11.77 20.57 13.83 1.66 1.44 2.10 0.59 0.76 0.57
NR4A1 ENST00000360284 11.78 24.16 15.79 1.66 1.33 1.78 0.59 0.98 0.66
EYA2 ENST00000327619 11.78 22.26 14.80 1.67 1.53 1.95 0.59 0.83 0.62
SLC35F1 ENST00000360388 11.79 14.49 10.74 1.67 2.02 2.19 0.59 0.61 0.43
UPF2 ENST00000356352 11.79 1.08 3.79 1.67 4.04 3.79 0.59 0.28 0.24
BEGAIN ENST00000443071 11.80 9.28 7.90 1.67 2.47 2.61 0.59 0.47 0.35
PEX5L ENST00000467460 11.80 24.23 15.84 1.67 1.32 1.77 0.60 0.98 0.66
CALU ENST00000542996 11.81 36.85 22.51 1.66 0.76 1.16 0.60 1.67 0.97
ATP6V0D1 ENST00000290949 11.81 11.62 9.14 1.66 2.09 2.35 0.60 0.57 0.38
TNR ENST00000367674 11.82 14.75 10.90 1.66 1.96 2.21 0.60 0.62 0.44
PHF12 ENST00000332830 11.82 2.27 4.31 1.64 3.64 3.75 0.60 0.29 0.24
XRN2 ENST00000377191 11.83 14.81 10.94 1.64 1.94 2.23 0.60 0.62 0.44
COL1A1 ENST00000225964 11.83 1.27 3.90 1.64 3.98 3.76 0.60 0.27 0.23
CSE1L ENST00000262982 11.84 1.63 4.04 1.64 3.86 3.75 0.60 0.26 0.23
IRF2BP1 ENST00000302165 11.84 9.46 8.02 1.64 2.48 2.59 0.60 0.49 0.37
TSPAN14 ENST00000429989 11.85 12.62 9.74 1.64 2.10 2.26 0.60 0.58 0.40
TUBG2 ENST00000251412 11.85 44.25 26.21 1.64 0.61 0.99 0.60 1.95 1.26
ELOVL1 ENST00000372458 11.86 22.39 14.88 1.63 1.51 1.94 0.61 0.82 0.63
LZIC ENST00000377223 11.86 66.64 37.49 1.63 0.54 0.84 0.61 1.22 2.01
MFN2 ENST00000235329 11.87 12.21 9.50 1.63 2.07 2.30 0.61 0.59 0.40
SETBP1 ENST00000282030 11.87 1.36 3.95 1.63 3.96 3.76 0.60 0.27 0.23
ABLIM1 ENST00000277895 11.88 14.72 10.93 1.63 1.97 2.23 0.59 0.62 0.44

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