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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
TLR3 ENST00000296795 52.69 43.14 46.60 0.67 0.62 0.66 1.77 1.89 1.89
LAMB3 ENST00000391911 52.69 38.94 44.28 0.67 0.70 0.61 1.77 1.64 2.04
VTI1B ENST00000554659 52.70 42.64 46.36 0.67 0.59 0.67 1.77 1.90 1.90
CLDN18 ENST00000183605 52.70 70.72 62.64 0.67 0.48 0.48 1.77 1.09 1.40
HIST1H4I ENST00000354348 52.71 95.51 77.26 0.67 0.23 0.35 1.77 0.21 0.58
KCNRG ENST00000312942 52.71 84.85 71.25 0.67 0.27 0.44 1.77 0.42 0.87
RAB27B ENST00000262094 52.72 45.74 48.05 0.67 0.75 0.67 1.77 2.02 1.88
RGS5 ENST00000530507 52.72 75.08 65.46 0.67 0.51 0.52 1.77 0.91 1.30
XYLB ENST00000207870 52.73 68.72 61.39 0.67 0.53 0.44 1.77 1.17 1.48
PPIF ENST00000225174 52.73 75.88 65.95 0.67 0.43 0.51 1.77 0.88 1.23
MED29 ENST00000315588 52.74 67.74 60.83 0.67 0.52 0.43 1.77 1.19 1.61
ZFAND2B ENST00000289528 52.75 55.47 53.51 0.67 0.57 0.63 1.77 1.60 1.82
SPATA6 ENST00000371847 52.75 77.28 66.74 0.67 0.42 0.54 1.77 0.77 1.20
SPC24 ENST00000592540 52.76 70.14 62.29 0.67 0.53 0.49 1.77 1.12 1.42
EVI2A ENST00000247270 52.76 77.69 66.96 0.67 0.42 0.53 1.77 0.79 1.19
PCDHA11 ENST00000398640 52.77 64.00 58.45 0.66 0.48 0.52 1.77 1.20 1.65
DPY19L2 ENST00000324472 52.77 45.42 47.93 0.66 0.68 0.66 1.77 2.01 1.88
HOXA6 ENST00000222728 52.78 81.52 69.26 0.66 0.33 0.44 1.77 0.53 0.97
TAGLN ENST00000532870 52.78 52.69 51.94 0.66 0.67 0.62 1.77 1.80 1.93
OBFC1 ENST00000224950 52.79 70.34 62.40 0.66 0.52 0.48 1.77 1.09 1.41
UPK2 ENST00000264031 52.79 93.70 76.38 0.66 0.28 0.37 1.77 0.27 0.61
SEMA4B ENST00000411539 52.80 28.70 39.10 0.66 1.16 0.77 1.77 1.29 2.06
PLEKHG1 ENST00000367328 52.80 19.31 34.33 0.66 1.46 0.87 1.77 0.76 1.77
DDX55 ENST00000238146 52.81 48.33 49.50 0.66 0.63 0.67 1.77 2.01 1.84
DCDC2 ENST00000378454 52.81 65.42 59.34 0.66 0.53 0.51 1.77 1.25 1.69

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