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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
GABPB1 ENST00000220429 1.43 12.85 4.42 4.31 2.07 3.72 0.20 0.59 0.25
MAPK8 ENST00000374189 1.43 6.23 1.70 4.31 2.73 4.25 0.20 0.36 0.23
POU3F2 ENST00000328345 1.44 17.55 6.84 4.31 1.58 2.94 0.21 0.72 0.33
ATP2B1 ENST00000428670 1.44 0.82 0.22 4.32 4.09 4.85 0.21 0.28 0.18
NFIX ENST00000397661 1.45 3.01 0.73 4.32 3.48 4.59 0.21 0.28 0.20
KCNB2 ENST00000523207 1.45 9.81 3.07 4.32 2.40 3.94 0.21 0.49 0.23
KAT7 ENST00000259021 1.46 2.06 0.49 4.31 3.71 4.73 0.21 0.29 0.17
RAP1A ENST00000369709 1.46 27.94 12.30 4.31 1.20 2.25 0.21 1.19 0.50
AKT3 ENST00000366539 1.47 4.58 1.18 4.31 3.24 4.42 0.20 0.32 0.21
RPS3 ENST00000278572 1.47 18.58 7.40 4.30 1.49 2.80 0.20 0.76 0.34
RPL38 ENST00000311111 1.48 28.97 12.77 4.30 1.15 2.11 0.20 1.31 0.52
FBXW11 ENST00000265094 1.48 13.12 4.65 4.32 2.07 3.68 0.20 0.60 0.25
SNRPC ENST00000244520 1.49 28.32 12.45 4.31 1.16 2.23 0.20 1.22 0.50
SMU1 ENST00000397149 1.49 1.36 0.33 4.31 3.96 4.83 0.20 0.27 0.18
TBL1XR1 ENST00000430069 1.50 1.41 0.34 4.31 3.95 4.81 0.20 0.27 0.18
PTP4A2 ENST00000344035 1.50 13.23 4.70 4.30 2.05 3.68 0.20 0.60 0.25
CNOT6L ENST00000264903 1.51 7.83 2.36 4.30 2.54 4.04 0.20 0.44 0.23
RTF1 ENST00000389629 1.51 0.59 0.18 4.30 4.14 4.87 0.20 0.28 0.18
CNOT7 ENST00000361272 1.52 4.27 1.09 4.29 3.25 4.42 0.20 0.32 0.21
ZBTB37 ENST00000367701 1.52 14.61 5.36 4.29 2.02 3.53 0.20 0.61 0.25
TUBB2A ENST00000333628 1.53 16.24 6.15 4.28 1.80 3.20 0.20 0.69 0.30
TCF4 ENST00000398339 1.53 6.52 1.86 4.28 2.63 4.19 0.20 0.37 0.24
KCNA3 ENST00000369769 1.54 19.54 7.90 4.28 1.43 2.61 0.20 0.74 0.35
HNRNPA1 ENST00000340913 1.54 3.24 0.79 4.27 3.46 4.55 0.20 0.28 0.21
AGO3 ENST00000373191 1.55 5.45 1.49 4.27 3.04 4.35 0.20 0.33 0.22

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