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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
NEK5 ENST00000355568 68.05 62.59 67.05 0.57 0.52 0.52 1.02 1.31 1.17
ITGAD ENST00000389202 68.06 47.48 57.78 0.57 0.63 0.51 1.02 2.01 1.67
NDUFB6 ENST00000379847 68.06 77.26 75.65 0.57 0.42 0.38 1.02 0.78 0.64
IGFBP6 ENST00000301464 68.07 52.48 60.90 0.57 0.66 0.43 1.02 1.83 1.59
ZNF585A ENST00000292841 68.07 36.30 51.29 0.57 0.82 0.63 1.02 1.60 1.92
SIRPA ENST00000358771 68.08 16.55 40.53 0.57 1.78 0.80 1.02 0.69 2.04
RPP21 ENST00000433076 68.09 81.35 77.91 0.57 0.33 0.38 1.02 0.54 0.54
ALDH3A1 ENST00000457500 68.09 80.91 77.69 0.57 0.35 0.38 1.02 0.57 0.55
FANCE ENST00000229769 68.10 44.70 56.12 0.57 0.66 0.49 1.02 1.97 1.76
MXD4 ENST00000337190 68.10 16.18 40.40 0.57 1.81 0.80 1.02 0.69 2.01
OR2F1 ENST00000392899 68.11 90.09 82.51 0.57 0.25 0.33 1.02 0.37 0.43
SPERT ENST00000310521 68.11 58.76 64.85 0.57 0.54 0.51 1.02 1.43 1.34
OR2F2 ENST00000408955 68.12 85.70 80.23 0.57 0.27 0.37 1.02 0.44 0.51
ACAA2 ENST00000285093 68.12 72.32 72.97 0.57 0.51 0.40 1.02 1.03 0.81
HOXA4 ENST00000360046 68.13 83.02 78.81 0.57 0.32 0.39 1.02 0.49 0.52
CHDH ENST00000315251 68.13 49.18 58.76 0.57 0.66 0.52 1.02 2.04 1.65
C17orf103 ENST00000399011 68.14 47.11 57.58 0.57 0.67 0.51 1.02 2.01 1.67
ALOX15B ENST00000380183 68.14 66.23 69.31 0.57 0.53 0.43 1.02 1.20 0.98
PRR5 ENST00000403581 68.15 29.10 47.39 0.57 1.14 0.65 1.02 1.33 1.86
GPLD1 ENST00000230036 68.15 45.11 56.43 0.57 0.68 0.52 1.02 1.97 1.71
ATXN1L ENST00000427980 68.16 8.25 36.34 0.57 2.56 0.85 1.02 0.45 1.86
TMEM14C ENST00000541412 68.16 75.85 74.94 0.57 0.43 0.40 1.02 0.88 0.64
BCMO1 ENST00000258168 68.17 65.79 69.07 0.56 0.54 0.44 1.02 1.22 1.02
ACTL7B ENST00000374667 68.17 81.92 78.30 0.56 0.35 0.38 1.02 0.51 0.54
OR10W1 ENST00000395079 68.18 83.67 79.25 0.56 0.27 0.38 1.02 0.47 0.54

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