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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
LRRC23 ENST00000007969 40.00 68.09 53.46 0.86 0.52 0.62 1.76 1.20 1.83
KRT33A ENST00000007735 63.50 86.86 78.43 0.59 0.22 0.38 1.24 0.40 0.54
ITGA3 ENST00000007722 31.47 26.63 27.20 0.94 1.20 0.99 1.68 1.12 1.25
YBX2 ENST00000007699 7.90 3.10 2.89 2.67 3.45 4.01 0.41 0.28 0.23
OSBPL7 ENST00000007414 28.10 22.76 23.52 1.16 1.46 1.18 1.48 0.89 1.00
TSR3 ENST00000007390 85.36 64.38 78.11 0.28 0.49 0.39 0.47 1.22 0.55
RHBDD2 ENST00000006777 49.46 27.61 36.69 0.56 1.27 0.82 1.80 1.17 1.93
CEACAM7 ENST00000006724 95.68 79.45 90.64 0.11 0.38 0.15 0.12 0.67 0.20
SPATA20 ENST00000006658 53.53 37.01 43.62 0.62 0.77 0.59 1.76 1.68 2.01
TRAPPC6A ENST00000006275 78.77 94.41 89.70 0.35 0.23 0.18 0.65 0.24 0.23
COPZ2 ENST00000006101 71.78 84.37 81.42 0.34 0.29 0.37 0.83 0.44 0.48
CX3CL1 ENST00000006053 98.52 19.84 59.42 0.10 1.42 0.49 0.11 0.74 1.71
HOXA11 ENST00000006015 12.53 14.20 11.01 1.67 2.06 2.20 0.63 0.60 0.44
PRSS21 ENST00000005995 97.96 70.97 87.60 0.11 0.49 0.27 0.11 1.06 0.31
RPAP3 ENST00000005386 37.98 31.43 32.89 0.92 0.96 0.86 1.72 1.42 1.67
DVL2 ENST00000005340 51.00 34.61 41.01 0.62 0.80 0.76 1.85 1.54 2.04
TMEM132A ENST00000005286 57.99 42.77 49.28 0.56 0.62 0.70 1.52 1.91 1.85
CACNG3 ENST00000005284 3.68 6.67 2.67 3.81 2.66 4.01 0.31 0.37 0.23
BAIAP2L1 ENST00000005260 50.07 35.32 40.88 0.54 0.77 0.78 1.81 1.58 2.06
RALA ENST00000005257 1.62 10.04 3.26 4.30 2.35 3.88 0.20 0.49 0.24
USH1C ENST00000005226 35.93 47.69 40.10 0.94 0.61 0.82 1.87 1.97 1.99
PDK4 ENST00000005178 47.32 70.12 58.81 0.56 0.53 0.51 1.82 1.12 1.65
SENP1 ENST00000004980 9.18 9.25 6.56 2.28 2.47 3.01 0.47 0.47 0.32
CCL18 ENST00000004921 79.50 89.41 87.59 0.34 0.27 0.27 0.57 0.37 0.31
SLC7A2 ENST00000004531 65.78 55.78 61.46 0.59 0.52 0.44 1.06 1.58 1.47

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