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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
DDX46 ENST00000354283 1.17 3.18 0.67 4.39 3.47 4.62 0.17 0.28 0.20
LUC7L3 ENST00000505658 1.17 0.85 0.14 4.39 4.11 4.85 0.17 0.28 0.18
UBE2E1 ENST00000306627 1.18 29.29 12.78 4.39 1.14 2.11 0.17 1.35 0.52
SUV39H2 ENST00000354919 1.18 15.72 5.70 4.40 1.87 3.31 0.17 0.69 0.28
PPP2R5E ENST00000337537 1.19 1.17 0.22 4.40 4.02 4.85 0.17 0.28 0.18
CASK ENST00000378166 1.19 0.42 0.09 4.39 4.13 4.87 0.17 0.28 0.16
PABPN1 ENST00000216727 1.20 28.38 12.37 4.39 1.16 2.23 0.17 1.22 0.50
PPP3R1 ENST00000234310 1.20 34.58 15.70 4.39 0.80 1.77 0.17 1.54 0.66
KLF7 ENST00000309446 1.21 9.26 2.72 4.40 2.47 4.00 0.17 0.46 0.23
RARG ENST00000425354 1.21 8.32 2.43 4.40 2.52 4.02 0.17 0.45 0.23
OTUD5 ENST00000156084 1.22 4.37 1.03 4.40 3.27 4.45 0.17 0.32 0.21
STAT3 ENST00000264657 1.22 0.95 0.20 4.39 4.08 4.87 0.17 0.29 0.18
BRD4 ENST00000263377 1.23 0.09 0.05 4.39 4.13 4.86 0.17 0.27 0.15
UBE2B ENST00000265339 1.23 39.18 18.16 4.41 0.70 1.66 0.17 1.61 0.79
GABRA1 ENST00000428797 1.24 11.67 3.81 4.42 2.10 3.78 0.17 0.57 0.24
PCGF1 ENST00000233630 1.24 4.14 0.99 4.42 3.26 4.46 0.17 0.32 0.21
PHYHIP ENST00000454243 1.25 22.44 9.30 4.42 1.52 2.32 0.17 0.82 0.38
ARF5 ENST00000000233 1.26 14.93 5.39 4.41 1.94 3.50 0.17 0.63 0.25
SCN2A ENST00000357398 1.26 2.31 0.51 4.41 3.64 4.71 0.17 0.29 0.17
USP46 ENST00000441222 1.27 15.42 5.63 4.40 1.89 3.38 0.17 0.67 0.27
ZBTB16 ENST00000335953 1.27 5.25 1.31 4.40 3.14 4.36 0.17 0.32 0.22
PAK3 ENST00000360648 1.28 11.61 3.80 4.40 2.10 3.78 0.17 0.57 0.24
C6orf106 ENST00000374023 1.28 13.08 4.46 4.39 2.06 3.71 0.17 0.59 0.25
SF3A3 ENST00000373019 1.29 1.72 0.37 4.39 3.84 4.79 0.17 0.26 0.18
ZRANB2 ENST00000370920 1.29 4.67 1.16 4.39 3.27 4.42 0.17 0.31 0.20

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