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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
PHLPP1 ENST00000262719 45.72 9.66 25.81 0.57 2.45 1.01 1.76 0.50 1.23
YIF1B ENST00000339413 45.72 60.54 52.40 0.57 0.52 0.61 1.77 1.41 1.91
TBC1D2B ENST00000300584 45.73 36.30 39.39 0.58 0.82 0.78 1.77 1.61 2.04
TGM5 ENST00000220420 45.73 77.08 62.24 0.58 0.42 0.48 1.77 0.78 1.43
TOR1AIP1 ENST00000606911 45.74 51.45 47.35 0.58 0.63 0.66 1.77 1.89 1.86
TRMT10A ENST00000273962 45.74 69.45 57.56 0.58 0.54 0.51 1.77 1.12 1.66
NOL6 ENST00000297990 45.75 5.43 23.69 0.58 3.02 1.15 1.77 0.33 1.02
ORMDL1 ENST00000325795 45.75 63.75 54.29 0.58 0.49 0.59 1.77 1.22 1.73
ANKAR ENST00000520309 45.76 60.10 52.16 0.58 0.52 0.61 1.77 1.39 1.90
COL4A4 ENST00000396625 45.76 31.33 36.70 0.58 0.97 0.82 1.77 1.39 1.93
ADRB1 ENST00000369295 45.77 79.76 64.04 0.58 0.37 0.53 1.77 0.64 1.39
ZNF454 ENST00000320129 45.77 50.23 46.68 0.58 0.67 0.66 1.77 1.99 1.87
RRP12 ENST00000370992 45.78 29.28 35.66 0.58 1.14 0.85 1.77 1.35 1.77
EFNA1 ENST00000368407 45.78 32.92 37.61 0.58 0.82 0.82 1.78 1.46 2.01
RCE1 ENST00000309657 45.79 32.02 37.15 0.58 0.92 0.81 1.78 1.48 1.97
TMEM136 ENST00000314475 45.79 67.20 56.26 0.58 0.54 0.49 1.78 1.22 1.76
ENTPD7 ENST00000370489 45.80 45.91 44.34 0.58 0.75 0.61 1.78 2.03 2.04
TXLNG ENST00000380122 45.80 3.37 22.75 0.58 3.43 1.18 1.78 0.29 0.98
DKK1 ENST00000373970 45.81 38.51 40.43 0.58 0.73 0.80 1.78 1.68 2.02
GPR1 ENST00000407325 45.81 78.44 63.23 0.58 0.43 0.49 1.78 0.73 1.36
SLC7A10 ENST00000253188 45.82 42.86 42.62 0.58 0.62 0.67 1.78 1.92 2.02
TEFM ENST00000581216 45.82 32.11 37.30 0.58 0.89 0.84 1.78 1.46 2.01
DNAI1 ENST00000242317 45.83 37.27 39.89 0.58 0.76 0.78 1.78 1.66 2.02
NGF ENST00000369512 45.83 33.37 37.82 0.59 0.85 0.84 1.78 1.51 2.01
CIB1 ENST00000328649 45.84 63.29 54.07 0.59 0.47 0.59 1.78 1.31 1.77

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