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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
ZNF679 ENST00000421025 94.53 62.52 81.89 0.10 0.53 0.37 0.11 1.31 0.46
CD200R1L ENST00000398214 94.53 51.94 76.33 0.10 0.61 0.35 0.11 1.85 0.61
ARTN ENST00000414809 94.54 57.46 79.31 0.10 0.56 0.39 0.11 1.48 0.53
LILRA1 ENST00000251372 94.54 82.25 91.31 0.10 0.34 0.15 0.11 0.52 0.18
P2RY11 ENST00000321826 94.55 90.17 95.10 0.10 0.25 0.09 0.11 0.38 0.10
CR1L ENST00000508064 94.55 82.68 91.48 0.10 0.34 0.15 0.12 0.50 0.18
NPIPB15 ENST00000429990 94.56 93.37 96.76 0.10 0.28 0.08 0.12 0.28 0.08
SPANXD ENST00000370515 94.56 94.88 97.36 0.10 0.23 0.08 0.12 0.23 0.07
LRRC37A ENST00000320254 94.57 43.65 71.69 0.10 0.62 0.44 0.12 1.97 0.82
GOLGA8B ENST00000267731 94.57 87.93 94.03 0.10 0.25 0.09 0.12 0.37 0.12
ZNF778 ENST00000433976 94.58 85.79 92.92 0.10 0.28 0.14 0.12 0.44 0.15
GOLGA6B ENST00000421285 94.58 84.72 92.34 0.10 0.27 0.14 0.12 0.42 0.15
ZNF343 ENST00000278772 94.59 79.56 90.15 0.10 0.38 0.18 0.12 0.66 0.21
PYDC2 ENST00000518817 94.59 99.66 99.07 0.10 0.17 0.11 0.12 0.12 0.04
ZNF543 ENST00000321545 94.60 85.59 92.85 0.10 0.27 0.14 0.12 0.44 0.15
ZNF658 ENST00000602553 94.60 91.41 95.78 0.10 0.23 0.07 0.12 0.33 0.11
TMEM194B ENST00000409150 94.61 54.97 77.97 0.10 0.57 0.38 0.12 1.63 0.54
C9orf66 ENST00000382387 94.61 93.31 96.76 0.10 0.28 0.08 0.12 0.29 0.08
TMEM86B ENST00000327042 94.62 95.50 97.64 0.10 0.23 0.09 0.12 0.21 0.06
OAS2 ENST00000342315 94.62 69.24 85.26 0.10 0.57 0.34 0.12 1.14 0.36
C3orf22 ENST00000318225 94.63 53.96 77.52 0.10 0.65 0.35 0.12 1.70 0.57
FCRL3 ENST00000368184 94.63 72.40 86.70 0.10 0.51 0.30 0.11 1.03 0.33
SIRPB1 ENST00000381605 94.64 83.91 92.02 0.10 0.28 0.14 0.11 0.47 0.16
TGIF2LY ENST00000321217 94.64 99.39 99.07 0.10 0.16 0.11 0.11 0.12 0.04
HTN1 ENST00000511674 94.65 87.40 93.81 0.10 0.23 0.10 0.11 0.41 0.13

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