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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
RRM1 ENST00000300738 5.05 0.32 0.98 3.52 4.14 4.44 0.30 0.28 0.21
RANBP9 ENST00000011619 6.40 0.62 1.51 3.04 4.14 4.33 0.36 0.28 0.22
RTF1 ENST00000389629 1.51 0.59 0.18 4.30 4.14 4.87 0.20 0.28 0.18
ZC3H4 ENST00000253048 44.50 0.20 20.45 0.63 4.14 1.49 1.78 0.28 0.89
MATR3 ENST00000394805 3.22 0.53 0.54 3.87 4.14 4.71 0.30 0.27 0.17
KMT2D ENST00000301067 11.45 0.50 3.43 1.73 4.14 3.86 0.58 0.28 0.23
SIN3A ENST00000394947 4.93 0.41 0.95 3.57 4.14 4.47 0.30 0.28 0.21
KMT2A ENST00000534358 5.67 0.35 1.18 3.19 4.14 4.43 0.33 0.28 0.21
CHERP ENST00000546361 8.94 0.32 2.31 2.35 4.14 4.03 0.45 0.28 0.22
TEX11 ENST00000395889 78.52 0.62 37.78 0.34 4.14 0.84 0.66 0.28 2.01
RB1 ENST00000267163 10.79 0.59 3.12 1.92 4.14 3.93 0.57 0.28 0.24
ARID1A ENST00000324856 13.75 0.19 4.26 1.64 4.15 3.76 0.69 0.28 0.24
RABGAP1 ENST00000373647 4.05 0.53 0.77 3.75 4.15 4.56 0.29 0.27 0.21
SUPT5H ENST00000599117 5.96 0.50 1.28 3.06 4.15 4.37 0.34 0.28 0.21
JMJD1C ENST00000399262 14.11 0.40 4.58 1.63 4.15 3.70 0.71 0.28 0.25
WDFY3 ENST00000295888 6.25 0.34 1.33 3.04 4.15 4.34 0.35 0.28 0.22
NAV1 ENST00000367296 5.33 0.61 1.14 3.37 4.15 4.41 0.32 0.28 0.21
OGT ENST00000373719 0.23 0.58 0.03 4.48 4.15 4.89 0.16 0.28 0.15
SUV420H1 ENST00000304363 2.91 0.52 0.45 3.92 4.15 4.73 0.30 0.27 0.17
TNPO1 ENST00000337273 2.61 0.19 0.30 4.03 4.15 4.85 0.28 0.28 0.18
FXR1 ENST00000357559 2.62 0.49 0.40 4.02 4.15 4.78 0.28 0.28 0.18
CREBBP ENST00000262367 6.74 0.34 1.54 2.99 4.15 4.32 0.37 0.28 0.22
HIVEP2 ENST00000367603 12.40 0.61 3.84 1.66 4.15 3.76 0.61 0.28 0.24
RBBP6 ENST00000319715 8.66 0.58 2.29 2.42 4.15 4.05 0.44 0.28 0.23
TM9SF2 ENST00000376387 3.39 0.55 0.57 3.83 4.15 4.71 0.30 0.27 0.17

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