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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
GSTZ1 ENST00000216465 60.95 80.27 73.43 0.57 0.37 0.42 1.35 0.58 0.76
RENBP ENST00000393700 60.96 24.36 40.84 0.57 1.32 0.80 1.35 1.00 2.04
ASB2 ENST00000555019 60.96 66.73 65.40 0.57 0.56 0.53 1.34 1.21 1.32
CNTLN ENST00000380647 60.97 63.28 63.21 0.57 0.47 0.49 1.34 1.31 1.36
B9D2 ENST00000243578 60.97 81.66 74.16 0.57 0.33 0.39 1.34 0.52 0.69
RSL24D1 ENST00000260443 60.98 22.24 39.95 0.57 1.53 0.81 1.34 0.81 2.01
TMEM102 ENST00000323206 60.98 56.22 58.70 0.57 0.52 0.52 1.34 1.56 1.65
SOGA2 ENST00000359865 60.99 21.98 39.84 0.58 1.48 0.77 1.34 0.81 2.03
MRPS27 ENST00000261413 60.99 46.15 52.94 0.58 0.73 0.61 1.34 2.04 1.87
STX18 ENST00000306200 61.00 52.26 56.42 0.58 0.62 0.52 1.34 1.84 1.72
CERCAM ENST00000372838 61.00 45.92 52.77 0.58 0.76 0.61 1.34 2.02 1.89
CEP44 ENST00000457424 61.01 60.66 61.54 0.58 0.54 0.46 1.33 1.41 1.48
IGSF9 ENST00000368094 61.01 40.75 49.86 0.58 0.62 0.63 1.33 1.78 1.89
CACNG5 ENST00000533854 61.02 50.78 55.58 0.58 0.63 0.53 1.34 1.94 1.74
MOS ENST00000311923 61.02 36.13 47.32 0.58 0.82 0.66 1.34 1.60 1.87
MCM10 ENST00000484800 61.03 45.22 52.38 0.59 0.70 0.61 1.34 1.98 1.90
ADIPOQ ENST00000412955 61.04 94.25 80.98 0.59 0.24 0.39 1.34 0.25 0.50
CWC25 ENST00000225428 61.04 42.16 50.63 0.59 0.62 0.66 1.34 1.87 1.85
STX19 ENST00000315099 61.05 85.58 76.42 0.59 0.27 0.38 1.34 0.44 0.61
EPHA8 ENST00000166244 61.05 35.79 47.18 0.59 0.78 0.67 1.34 1.59 1.89
PDCD1 ENST00000334409 61.06 33.81 46.14 0.59 0.85 0.67 1.34 1.55 1.97
BCL2L15 ENST00000393316 61.06 60.61 61.54 0.59 0.53 0.46 1.34 1.41 1.48
LIMS2 ENST00000324938 61.07 48.49 54.31 0.59 0.65 0.59 1.34 2.02 1.73
PAFAH2 ENST00000374282 61.07 61.24 61.92 0.59 0.53 0.48 1.33 1.40 1.45
RAB21 ENST00000261263 61.08 35.73 47.13 0.59 0.78 0.67 1.33 1.58 1.90

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