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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
LENG8 ENST00000326764 35.90 7.74 19.89 0.94 2.54 1.47 1.89 0.43 0.84
SFXN3 ENST00000224807 35.91 69.46 51.85 0.94 0.54 0.62 1.88 1.13 1.92
CASKIN1 ENST00000343516 35.91 4.03 17.91 0.94 3.25 1.68 1.88 0.32 0.77
ACOT6 ENST00000381139 35.92 84.34 60.68 0.94 0.28 0.44 1.88 0.44 1.61
CCDC42 ENST00000293845 35.92 62.13 47.92 0.94 0.54 0.66 1.88 1.35 1.89
LRRC39 ENST00000370138 35.93 44.01 38.26 0.94 0.61 0.85 1.88 1.97 2.04
USH1C ENST00000005226 35.93 47.69 40.10 0.94 0.61 0.82 1.87 1.97 1.99
GOLGA7B ENST00000370602 35.94 57.45 45.41 0.94 0.56 0.70 1.87 1.48 2.01
SPDEF ENST00000374037 35.94 13.42 22.87 0.94 2.05 1.19 1.87 0.61 0.97
TOPBP1 ENST00000260810 35.95 0.77 16.18 0.94 4.12 1.71 1.87 0.27 0.66
NDUFS1 ENST00000455934 35.95 43.86 38.18 0.94 0.61 0.85 1.87 1.97 2.04
BCL7C ENST00000215115 35.96 43.45 37.94 0.94 0.61 0.85 1.87 1.95 2.02
HOOK1 ENST00000371208 35.96 29.94 31.14 0.94 1.10 0.85 1.87 1.41 1.55
BMPER ENST00000297161 35.97 34.19 33.21 0.94 0.84 0.87 1.87 1.55 1.68
CPLX4 ENST00000299721 35.97 89.24 63.89 0.94 0.27 0.51 1.87 0.36 1.39
TMEM87B ENST00000283206 35.98 52.38 42.44 0.94 0.62 0.68 1.87 1.82 2.01
ZMYND10 ENST00000231749 35.98 46.84 39.77 0.94 0.71 0.80 1.87 1.97 2.04
ZCCHC3 ENST00000382352 35.99 64.33 49.06 0.94 0.49 0.72 1.87 1.20 1.83
WBP4 ENST00000379487 36.00 56.76 45.02 0.94 0.53 0.70 1.87 1.55 2.04
DISP2 ENST00000267889 36.00 19.39 25.82 0.94 1.47 1.01 1.87 0.74 1.23
FBXO48 ENST00000377957 36.01 87.07 62.38 0.94 0.22 0.48 1.87 0.40 1.41
WASF3 ENST00000335327 36.01 22.72 27.46 0.94 1.47 0.96 1.87 0.88 1.27
MRPL17 ENST00000288937 36.02 73.07 54.03 0.94 0.52 0.59 1.87 1.02 1.76
RIOK2 ENST00000283109 36.02 39.45 35.82 0.94 0.70 0.86 1.86 1.64 1.79
FAM63B ENST00000559228 36.03 33.92 33.12 0.94 0.84 0.87 1.86 1.56 1.69

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