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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
MTRNR2L10 ENST00000545075 94.01 99.82 98.95 0.10 0.17 0.10 0.13 0.11 0.04
RNASE3 ENST00000304639 97.42 99.82 99.76 0.10 0.17 0.12 0.11 0.11 0.04
MAS1L ENST00000377127 99.39 99.83 99.98 0.11 0.17 0.13 0.12 0.11 0.04
KRTAP4-16P ENST00000440582 85.83 99.83 95.63 0.27 0.17 0.08 0.45 0.11 0.11
DEFB107B ENST00000355602 94.02 99.84 97.73 0.10 0.17 0.09 0.13 0.11 0.05
ADAM20 ENST00000256389 96.83 99.85 99.63 0.09 0.17 0.12 0.11 0.11 0.04
USP17L10 ENST00000417945 94.07 99.85 98.82 0.11 0.17 0.10 0.13 0.11 0.05
MTRNR2L9 ENST00000544932 94.07 99.86 98.69 0.11 0.17 0.10 0.13 0.11 0.05
DIRC1 ENST00000308100 96.69 99.86 99.44 0.11 0.17 0.11 0.11 0.11 0.05
ATXN3L ENST00000380622 95.57 99.87 99.35 0.11 0.17 0.11 0.11 0.11 0.04
TAS2R20 ENST00000538986 96.95 99.87 99.33 0.09 0.17 0.11 0.11 0.11 0.04
OR7G1 ENST00000541538 98.26 99.88 99.87 0.09 0.17 0.12 0.10 0.11 0.04
PGAM4 ENST00000458128 78.57 99.88 91.97 0.34 0.17 0.14 0.66 0.11 0.16
MRGPRX3 ENST00000396275 95.80 99.89 99.42 0.11 0.17 0.11 0.11 0.11 0.05
RP11-1070N10.3 ENST00000554161 94.12 99.89 98.99 0.10 0.17 0.11 0.13 0.11 0.04
AL136531.1 ENST00000537552 94.12 99.90 98.68 0.10 0.17 0.10 0.13 0.11 0.05
RP11-863K10.7 ENST00000330539 94.14 99.90 99.00 0.10 0.17 0.11 0.13 0.10 0.04
TAS2R43 ENST00000531678 97.08 99.91 99.59 0.10 0.17 0.12 0.11 0.10 0.05
KRTAP12-3 ENST00000397907 85.34 99.91 95.24 0.28 0.17 0.08 0.47 0.10 0.10
PNMA3 ENST00000447306 96.24 99.92 99.54 0.12 0.17 0.12 0.11 0.10 0.05
OR7A5 ENST00000322301 82.46 99.92 93.99 0.30 0.17 0.09 0.56 0.10 0.11
C5orf20 ENST00000503143 96.73 99.93 99.63 0.11 0.17 0.12 0.11 0.10 0.04
FAM47C ENST00000358047 96.85 99.93 99.16 0.09 0.17 0.11 0.11 0.10 0.04
KRTAP19-1 ENST00000390689 96.12 99.94 99.14 0.11 0.17 0.11 0.11 0.10 0.04
MAGEA10 ENST00000370323 98.60 99.94 99.75 0.10 0.18 0.12 0.11 0.10 0.04

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