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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
ZNF728 ENST00000594710 97.06 88.33 95.46 0.10 0.23 0.08 0.11 0.37 0.11
SPATA31A1 ENST00000377647 96.33 89.07 95.47 0.12 0.27 0.08 0.11 0.35 0.11
MGC10955 ENST00000401851 91.65 98.53 97.06 0.14 0.21 0.08 0.20 0.15 0.07
C5orf47 ENST00000340147 90.80 93.45 95.47 0.16 0.28 0.08 0.21 0.28 0.11
OR14A2 ENST00000366485 92.39 98.97 97.06 0.15 0.17 0.08 0.18 0.15 0.07
BHLHA15 ENST00000609256 93.61 91.66 95.48 0.13 0.24 0.08 0.13 0.32 0.11
KRTAP20-4 ENST00000382828 90.37 97.89 97.07 0.15 0.21 0.08 0.25 0.17 0.07
C14orf79 ENST00000547315 95.87 89.55 95.48 0.11 0.27 0.08 0.11 0.36 0.11
XAGE5 ENST00000351072 96.82 91.83 97.07 0.09 0.23 0.08 0.11 0.32 0.07
PAPPA-AS1 ENST00000445861 92.25 92.76 95.49 0.15 0.29 0.08 0.18 0.30 0.11
C6orf141 ENST00000529246 86.56 98.67 95.49 0.24 0.20 0.08 0.41 0.15 0.11
AC025278.1 ENST00000377296 90.95 98.20 97.08 0.16 0.20 0.08 0.21 0.15 0.07
TSPYL6 ENST00000317802 86.32 98.58 95.50 0.25 0.20 0.08 0.42 0.15 0.11
TEX22 ENST00000451127 93.15 95.26 97.08 0.15 0.23 0.08 0.16 0.21 0.07
PNMAL2 ENST00000599531 86.72 97.91 95.50 0.24 0.20 0.08 0.40 0.17 0.11
GAGE10 ENST00000407599 95.73 92.94 97.09 0.11 0.29 0.08 0.12 0.30 0.07
TBC1D3F ENST00000327454 89.69 95.72 95.51 0.16 0.23 0.08 0.28 0.20 0.11
AP000679.2 ENST00000319763 90.38 97.91 97.09 0.15 0.20 0.08 0.25 0.17 0.07
ZNF582 ENST00000301310 98.73 86.78 95.51 0.10 0.24 0.08 0.11 0.40 0.11
MTRNR2L12 ENST00000600213 92.23 98.85 97.10 0.15 0.16 0.08 0.18 0.14 0.07
KRTAP19-2 ENST00000334055 87.28 98.08 95.52 0.23 0.20 0.08 0.38 0.16 0.11
FAM111A ENST00000528737 88.70 96.81 95.52 0.19 0.23 0.08 0.34 0.19 0.11
C8orf56 ENST00000436771 90.40 97.92 97.10 0.15 0.20 0.08 0.25 0.17 0.07
PUSL1 ENST00000379031 88.07 97.45 95.53 0.20 0.22 0.08 0.35 0.19 0.11
CTD-2054N24.2 ENST00000560059 91.46 96.84 97.11 0.15 0.23 0.08 0.20 0.19 0.07

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