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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
PHF21A ENST00000418153 2.46 0.55 0.37 4.10 4.17 4.78 0.27 0.27 0.18
ZMYND8 ENST00000461685 1.68 0.56 0.21 4.30 4.17 4.86 0.22 0.27 0.18
MBTD1 ENST00000586178 5.57 0.56 1.21 3.23 4.16 4.42 0.33 0.28 0.21
UBAP2L ENST00000428931 10.66 0.54 3.03 1.97 4.16 3.96 0.57 0.27 0.24
U2SURP ENST00000473835 1.83 0.57 0.25 4.28 4.16 4.82 0.22 0.28 0.18
PRKCB ENST00000303531 2.32 0.60 0.34 4.12 4.16 4.82 0.28 0.28 0.18
SPTBN1 ENST00000356805 5.57 0.51 1.20 3.23 4.16 4.43 0.33 0.27 0.21
MGA ENST00000219905 17.88 0.54 6.58 1.53 4.16 3.00 0.90 0.27 0.32
KHSRP ENST00000398148 7.63 0.57 1.93 2.73 4.16 4.15 0.40 0.28 0.24
SMARCAD1 ENST00000359052 5.87 0.60 1.30 3.16 4.16 4.36 0.33 0.28 0.22
TLE3 ENST00000558939 6.74 0.52 1.60 2.97 4.15 4.28 0.37 0.27 0.23
TM9SF2 ENST00000376387 3.39 0.55 0.57 3.83 4.15 4.71 0.30 0.27 0.17
RBBP6 ENST00000319715 8.66 0.58 2.29 2.42 4.15 4.05 0.44 0.28 0.23
HIVEP2 ENST00000367603 12.40 0.61 3.84 1.66 4.15 3.76 0.61 0.28 0.24
CREBBP ENST00000262367 6.74 0.34 1.54 2.99 4.15 4.32 0.37 0.28 0.22
FXR1 ENST00000357559 2.62 0.49 0.40 4.02 4.15 4.78 0.28 0.28 0.18
TNPO1 ENST00000337273 2.61 0.19 0.30 4.03 4.15 4.85 0.28 0.28 0.18
SUV420H1 ENST00000304363 2.91 0.52 0.45 3.92 4.15 4.73 0.30 0.27 0.17
OGT ENST00000373719 0.23 0.58 0.03 4.48 4.15 4.89 0.16 0.28 0.15
NAV1 ENST00000367296 5.33 0.61 1.14 3.37 4.15 4.41 0.32 0.28 0.21
WDFY3 ENST00000295888 6.25 0.34 1.33 3.04 4.15 4.34 0.35 0.28 0.22
JMJD1C ENST00000399262 14.11 0.40 4.58 1.63 4.15 3.70 0.71 0.28 0.25
SUPT5H ENST00000599117 5.96 0.50 1.28 3.06 4.15 4.37 0.34 0.28 0.21
RABGAP1 ENST00000373647 4.05 0.53 0.77 3.75 4.15 4.56 0.29 0.27 0.21
ARID1A ENST00000324856 13.75 0.19 4.26 1.64 4.15 3.76 0.69 0.28 0.24

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