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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
NUDT21 ENST00000300291 0.07 7.52 1.68 4.59 2.52 4.26 0.15 0.40 0.23
SNRK ENST00000296088 5.39 2.14 1.69 3.35 3.67 4.26 0.32 0.29 0.23
SYNCRIP ENST00000369622 1.33 6.27 1.69 4.36 2.72 4.25 0.18 0.36 0.23
TUBB2B ENST00000259818 0.30 7.28 1.70 4.44 2.58 4.25 0.17 0.37 0.23
MAPK8 ENST00000374189 1.43 6.23 1.70 4.31 2.73 4.25 0.20 0.36 0.23
NR2F2 ENST00000394166 0.94 6.70 1.71 4.39 2.66 4.24 0.18 0.37 0.23
PABPC1 ENST00000318607 2.53 5.13 1.71 4.07 3.20 4.24 0.28 0.33 0.23
SF3B3 ENST00000302516 3.20 4.44 1.72 3.87 3.27 4.24 0.30 0.32 0.23
SERBP1 ENST00000370995 2.74 4.93 1.73 4.01 3.26 4.24 0.29 0.32 0.23
HCFC1 ENST00000310441 7.37 0.30 1.73 2.86 4.11 4.23 0.39 0.29 0.23
MARK2 ENST00000402010 3.94 3.71 1.74 3.79 3.33 4.23 0.30 0.30 0.23
NLK ENST00000407008 5.81 1.87 1.74 3.18 3.76 4.23 0.33 0.26 0.23
ARID5B ENST00000279873 6.30 1.40 1.75 3.02 3.95 4.22 0.36 0.27 0.23
IRF6 ENST00000367021 5.44 2.31 1.75 3.31 3.63 4.22 0.33 0.29 0.23
SCN3A ENST00000283254 4.42 3.33 1.76 3.71 3.42 4.22 0.29 0.27 0.23
GABBR2 ENST00000259455 3.89 3.86 1.76 3.77 3.30 4.23 0.30 0.31 0.23
CFLAR ENST00000309955 3.87 3.90 1.77 3.77 3.29 4.23 0.30 0.31 0.23
CREB1 ENST00000432329 0.20 7.58 1.77 4.51 2.51 4.22 0.16 0.42 0.23
MTOR ENST00000361445 2.83 4.96 1.78 3.96 3.25 4.22 0.28 0.32 0.23
IPO7 ENST00000379719 6.56 1.28 1.78 3.00 3.97 4.24 0.37 0.27 0.23
FAF2 ENST00000261942 3.76 4.09 1.79 3.79 3.25 4.23 0.30 0.32 0.23
PSMD1 ENST00000308696 6.15 1.70 1.79 3.04 3.85 4.23 0.35 0.26 0.23
DKC1 ENST00000369550 2.79 5.07 1.80 3.98 3.21 4.23 0.28 0.33 0.23
MECOM ENST00000264674 5.43 2.44 1.80 3.34 3.59 4.22 0.32 0.29 0.23
GSK3A ENST00000222330 5.03 2.86 1.81 3.53 3.51 4.22 0.30 0.28 0.23

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