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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
HOXC10 ENST00000303460 51.14 38.08 42.93 0.61 0.77 0.67 1.85 1.70 1.99
PLBD2 ENST00000280800 51.14 57.04 53.49 0.61 0.56 0.63 1.85 1.52 1.82
EMC9 ENST00000419198 51.15 63.94 57.48 0.61 0.48 0.52 1.85 1.21 1.65
DPY19L1 ENST00000310974 51.15 25.72 36.55 0.59 1.24 0.85 1.85 1.05 1.90
COA4 ENST00000355693 51.16 76.93 65.62 0.59 0.43 0.51 1.85 0.79 1.29
FIS1 ENST00000223136 51.16 80.88 67.93 0.59 0.35 0.51 1.85 0.57 1.10
NDUFA6 ENST00000498737 51.17 85.50 70.66 0.59 0.27 0.43 1.85 0.45 0.88
ZFP36 ENST00000597629 51.18 26.48 37.05 0.59 1.16 0.80 1.85 1.10 1.95
APOB ENST00000233242 51.18 22.71 35.12 0.59 1.47 0.86 1.85 0.88 1.76
TP53RK ENST00000372114 51.19 83.99 69.80 0.59 0.28 0.44 1.85 0.46 0.93
RBP3 ENST00000224600 51.19 34.53 41.07 0.59 0.80 0.75 1.85 1.55 2.04
OR8A1 ENST00000284287 51.20 79.07 66.85 0.59 0.39 0.53 1.85 0.70 1.19
C18orf32 ENST00000318240 51.20 79.73 67.24 0.59 0.37 0.52 1.85 0.64 1.17
SDHAF2 ENST00000301761 51.21 88.75 72.66 0.59 0.25 0.43 1.85 0.36 0.81
EXOC3L2 ENST00000413988 51.21 22.82 35.22 0.59 1.44 0.86 1.85 0.89 1.75
JAKMIP3 ENST00000298622 51.22 14.01 30.86 0.59 2.06 0.77 1.84 0.59 1.49
ERMP1 ENST00000339450 51.22 47.64 48.30 0.59 0.62 0.67 1.84 1.97 1.89
TIMM23 ENST00000260867 51.23 60.87 55.74 0.59 0.56 0.53 1.84 1.41 1.74
DDX56 ENST00000258772 51.23 45.19 46.96 0.59 0.70 0.70 1.84 1.98 1.86
GLDC ENST00000321612 51.24 59.21 54.81 0.59 0.49 0.53 1.84 1.44 1.74
EMP3 ENST00000270221 51.24 80.42 67.69 0.59 0.37 0.52 1.84 0.59 1.12
FGD5 ENST00000285046 51.25 3.62 25.53 0.59 3.36 1.05 1.84 0.30 1.19
KIF12 ENST00000374118 51.25 50.29 49.70 0.59 0.67 0.66 1.85 1.97 1.85
BMP3 ENST00000282701 51.26 33.94 40.76 0.59 0.84 0.81 1.85 1.56 2.04
ARHGEF19 ENST00000270747 51.26 61.25 55.93 0.59 0.53 0.49 1.85 1.40 1.76

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