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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
LSM4 ENST00000593829 17.76 54.79 34.50 1.49 0.56 0.90 0.90 1.63 1.77
FGF21 ENST00000593756 74.60 71.30 75.97 0.38 0.53 0.38 0.79 1.07 0.62
EGLN2 ENST00000593726 35.41 21.64 26.66 0.96 1.44 0.99 1.87 0.81 1.25
AC007421.1 ENST00000593717 91.26 98.32 98.60 0.15 0.21 0.10 0.21 0.14 0.05
PAK4 ENST00000593690 64.34 43.39 53.30 0.56 0.61 0.62 1.19 1.95 1.85
DYRK1B ENST00000593685 9.40 10.26 7.19 2.23 2.28 2.85 0.47 0.50 0.34
AC093157.1 ENST00000593496 60.03 87.51 76.92 0.63 0.23 0.35 1.39 0.38 0.60
AC015989.2 ENST00000593319 93.51 99.61 97.88 0.13 0.16 0.09 0.14 0.12 0.04
FLJ14816 ENST00000593290 99.14 99.73 99.97 0.11 0.17 0.13 0.12 0.11 0.04
COX6B2 ENST00000593184 72.14 82.47 80.62 0.34 0.34 0.39 0.80 0.52 0.51
AC006132.1 ENST00000593161 92.71 96.85 96.97 0.15 0.23 0.08 0.17 0.19 0.07
KIF18B ENST00000593135 70.68 27.85 48.12 0.49 1.23 0.66 0.91 1.19 1.87
RAD51L3-RFFL ENST00000593039 29.25 60.71 43.37 1.09 0.54 0.63 1.57 1.39 2.01
HSPB6 ENST00000592984 90.89 73.31 84.91 0.16 0.56 0.34 0.20 1.02 0.40
PIGW ENST00000592983 52.94 56.83 54.44 0.65 0.56 0.57 1.76 1.54 1.75
RP11-15E18.4 ENST00000592917 90.98 95.33 96.13 0.16 0.24 0.07 0.21 0.21 0.10
ZNF266 ENST00000592904 98.42 76.03 90.26 0.10 0.43 0.16 0.11 0.86 0.22
C18orf21 ENST00000592875 40.90 80.23 61.24 0.84 0.37 0.43 1.72 0.58 1.49
ACP5 ENST00000592828 53.26 39.56 45.05 0.63 0.68 0.70 1.75 1.65 2.02
NMT1 ENST00000592782 4.87 11.08 5.24 3.59 2.09 3.56 0.31 0.53 0.26
FAM20A ENST00000592554 44.84 45.95 43.76 0.63 0.76 0.61 1.75 2.02 2.02
SPC24 ENST00000592540 52.76 70.14 62.29 0.67 0.53 0.49 1.77 1.12 1.42
IGFLR1 ENST00000592537 97.22 72.41 87.96 0.10 0.51 0.24 0.11 1.03 0.32
ZNF540 ENST00000592533 95.11 52.17 76.75 0.10 0.62 0.34 0.12 1.84 0.61
ZNF101 ENST00000592502 68.22 35.59 50.98 0.56 0.77 0.66 1.01 1.58 1.85

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