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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
TLE6 ENST00000246112 96.02 33.99 66.72 0.11 0.84 0.54 0.11 1.55 1.20
IGFLR1 ENST00000592537 97.22 72.41 87.96 0.10 0.51 0.24 0.11 1.03 0.32
TRIM31 ENST00000376734 97.82 52.62 78.46 0.11 0.68 0.38 0.11 1.81 0.54
APOBEC3F ENST00000308521 98.42 56.19 80.61 0.10 0.52 0.39 0.11 1.56 0.52
PRAMEF16 ENST00000376121 96.03 93.14 97.26 0.11 0.28 0.08 0.11 0.30 0.07
DEFB4A ENST00000302247 97.23 97.16 99.08 0.10 0.24 0.11 0.11 0.18 0.04
C20orf166 ENST00000370527 97.83 95.31 98.67 0.11 0.24 0.10 0.11 0.21 0.05
ZNF266 ENST00000592904 98.42 76.03 90.26 0.10 0.43 0.16 0.11 0.86 0.22
RP11-770J1.5 ENST00000534438 96.03 92.88 97.17 0.11 0.29 0.08 0.11 0.30 0.06
LRRC37B ENST00000341671 97.23 21.29 59.58 0.10 1.42 0.49 0.11 0.81 1.69
KRTAP21-2 ENST00000333892 97.83 98.82 99.67 0.11 0.16 0.12 0.11 0.14 0.04
ZNF490 ENST00000311437 96.04 77.53 89.88 0.11 0.42 0.18 0.11 0.79 0.23
DEFB121 ENST00000376314 98.43 93.79 98.39 0.10 0.27 0.10 0.11 0.26 0.05
ZNF721 ENST00000511833 97.24 93.13 97.76 0.10 0.28 0.09 0.11 0.30 0.04
KRTAP19-6 ENST00000334046 96.04 99.34 99.37 0.11 0.16 0.11 0.11 0.12 0.04
IFNA5 ENST00000259555 97.84 99.48 99.78 0.11 0.16 0.12 0.11 0.13 0.04
STATH ENST00000246895 98.43 89.50 96.79 0.10 0.27 0.08 0.11 0.36 0.08
TBC1D28 ENST00000345096 97.24 89.78 96.25 0.10 0.27 0.07 0.11 0.37 0.09
HHLA1 ENST00000434736 96.05 68.73 85.70 0.11 0.53 0.33 0.11 1.17 0.33
ZNF208 ENST00000397126 97.84 91.77 97.43 0.11 0.23 0.08 0.11 0.32 0.07
ZNF665 ENST00000396424 98.44 90.02 96.99 0.10 0.25 0.08 0.11 0.37 0.07
C7orf61 ENST00000332375 97.25 55.31 79.53 0.10 0.57 0.38 0.11 1.61 0.52
FAM47B ENST00000329357 96.05 99.77 99.48 0.11 0.17 0.11 0.11 0.11 0.05
TCEB3B ENST00000332567 97.85 100.00 99.86 0.11 0.18 0.12 0.11 0.09 0.04
EIF4E1B ENST00000318682 96.06 68.09 85.43 0.11 0.52 0.34 0.11 1.20 0.35

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