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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
SERPIND1 ENST00000215727 66.25 79.95 76.16 0.58 0.37 0.37 1.07 0.61 0.62
BCAT2 ENST00000316273 66.25 68.08 69.28 0.58 0.52 0.43 1.07 1.20 0.98
DMP1 ENST00000339673 66.26 62.45 65.94 0.58 0.53 0.51 1.07 1.31 1.23
PHYKPL ENST00000308158 66.26 75.46 73.62 0.58 0.46 0.40 1.07 0.90 0.74
GPC5 ENST00000377067 66.27 59.50 64.15 0.58 0.51 0.52 1.07 1.40 1.37
ATXN10 ENST00000252934 66.27 35.73 49.99 0.58 0.78 0.62 1.07 1.58 1.90
PHOX2A ENST00000298231 66.28 27.14 45.43 0.58 1.23 0.70 1.07 1.13 1.99
DUSP18 ENST00000334679 66.28 62.51 66.05 0.58 0.53 0.51 1.07 1.31 1.23
DBH ENST00000393056 66.29 54.71 61.10 0.58 0.58 0.43 1.07 1.64 1.53
MXRA7 ENST00000355797 66.29 83.97 78.38 0.58 0.28 0.38 1.07 0.46 0.54
EFCAB12 ENST00000505956 66.30 46.61 56.22 0.58 0.75 0.49 1.07 2.00 1.77
TMED1 ENST00000214869 66.30 87.26 80.11 0.58 0.22 0.35 1.07 0.41 0.52
SI ENST00000264382 66.31 56.20 62.01 0.58 0.52 0.49 1.06 1.56 1.44
DDX28 ENST00000332395 66.31 76.88 74.52 0.58 0.43 0.40 1.06 0.80 0.68
COL15A1 ENST00000375001 66.32 24.85 43.99 0.58 1.33 0.61 1.06 1.06 2.03
CDH15 ENST00000289746 66.32 58.62 63.70 0.58 0.54 0.49 1.06 1.42 1.40
COX6A1P2 ENST00000423336 66.33 83.14 77.92 0.58 0.29 0.38 1.06 0.49 0.54
LIPI ENST00000344577 66.33 87.29 80.15 0.58 0.22 0.35 1.06 0.41 0.53
FAM188B ENST00000265299 66.34 63.07 66.43 0.58 0.48 0.51 1.06 1.29 1.21
SPINK7 ENST00000274565 66.34 76.07 74.00 0.58 0.43 0.39 1.06 0.86 0.70
NAT9 ENST00000357814 66.35 67.51 68.97 0.58 0.54 0.46 1.06 1.20 1.04
CYP27A1 ENST00000258415 66.36 76.49 74.28 0.59 0.42 0.39 1.06 0.84 0.70
COL5A3 ENST00000264828 66.36 30.87 47.36 0.59 1.08 0.66 1.06 1.36 1.85
ABCB6 ENST00000265316 66.37 55.06 61.38 0.59 0.58 0.44 1.06 1.63 1.48
MLK4 ENST00000366624 66.37 37.38 50.94 0.59 0.76 0.66 1.06 1.66 1.85

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