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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
CSTF1 ENST00000217109 2.59 14.85 5.98 4.04 1.92 3.25 0.28 0.62 0.30
SATB1 ENST00000417717 2.59 11.52 4.32 4.03 2.11 3.75 0.28 0.57 0.24
PTEN ENST00000371953 2.60 19.46 8.38 4.03 1.44 2.51 0.28 0.74 0.37
DEDD ENST00000368006 2.60 13.62 5.44 4.03 2.05 3.44 0.28 0.59 0.26
TNPO1 ENST00000337273 2.61 0.19 0.30 4.03 4.15 4.85 0.28 0.28 0.18
WDTC1 ENST00000361771 2.61 7.74 2.67 4.02 2.54 4.01 0.28 0.43 0.23
FXR1 ENST00000357559 2.62 0.49 0.40 4.02 4.15 4.78 0.28 0.28 0.18
TM9SF3 ENST00000371142 2.62 0.85 0.46 4.02 4.11 4.75 0.28 0.28 0.17
RAP2A ENST00000245304 2.63 23.50 10.65 4.02 1.40 2.18 0.28 0.92 0.43
NAA10 ENST00000464845 2.63 26.36 12.06 4.01 1.18 2.29 0.28 1.08 0.48
HNRNPA2B1 ENST00000354667 2.64 6.82 2.41 4.01 2.63 4.03 0.28 0.37 0.23
CDYL ENST00000397588 2.64 9.14 3.33 4.01 2.48 3.89 0.28 0.47 0.23
PRPF6 ENST00000266079 2.65 20.76 9.12 4.00 1.46 2.37 0.28 0.81 0.38
SIAH2 ENST00000312960 2.65 30.07 14.05 4.00 1.08 2.04 0.28 1.41 0.60
TNNC1 ENST00000232975 2.66 17.01 7.21 4.00 1.62 2.83 0.28 0.73 0.34
PAPD5 ENST00000436909 2.67 6.24 2.17 4.00 2.73 4.06 0.28 0.36 0.23
DROSHA ENST00000511367 2.67 15.41 6.37 3.99 1.89 3.09 0.29 0.67 0.32
TLK1 ENST00000431350 2.68 3.83 1.31 3.99 3.31 4.35 0.29 0.31 0.22
MTPN ENST00000393085 2.68 26.42 12.12 3.99 1.16 2.28 0.29 1.09 0.48
DCUN1D1 ENST00000292782 2.69 10.63 3.99 4.00 2.14 3.76 0.29 0.51 0.23
AGO2 ENST00000220592 2.69 1.55 0.65 4.02 3.88 4.64 0.29 0.26 0.19
AMIGO1 ENST00000369864 2.70 9.00 3.28 4.01 2.44 3.90 0.29 0.47 0.24
THOC2 ENST00000245838 2.70 0.63 0.42 4.01 4.14 4.76 0.29 0.28 0.17
CTR9 ENST00000361367 2.71 2.39 0.88 4.01 3.62 4.50 0.29 0.29 0.21
ACTR3 ENST00000263238 2.71 1.75 0.72 4.02 3.83 4.60 0.29 0.26 0.20

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