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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
C17orf77 ENST00000392620 99.31 98.33 99.86 0.11 0.21 0.12 0.12 0.14 0.04
RFPL4B ENST00000441065 98.63 98.78 99.82 0.10 0.16 0.12 0.11 0.14 0.04
SPRR3 ENST00000331860 98.28 98.33 99.56 0.09 0.21 0.12 0.10 0.14 0.05
OR14K1 ENST00000283225 99.61 98.78 99.94 0.12 0.16 0.13 0.13 0.14 0.04
IFNA4 ENST00000421715 87.20 98.34 95.64 0.23 0.21 0.08 0.38 0.14 0.11
CKS1B ENST00000600888 91.28 98.34 97.72 0.15 0.21 0.09 0.20 0.14 0.05
AC107021.1 ENST00000422482 92.09 98.79 98.14 0.15 0.16 0.09 0.20 0.14 0.05
KRTAP19-7 ENST00000334849 84.69 98.35 94.17 0.29 0.21 0.09 0.47 0.14 0.12
IFNA13 ENST00000449498 95.54 98.79 99.11 0.11 0.16 0.11 0.11 0.14 0.04
FLJ00104 ENST00000446344 91.28 98.35 97.74 0.15 0.21 0.09 0.20 0.14 0.05
LCE4A ENST00000368777 81.37 98.80 93.26 0.33 0.16 0.14 0.60 0.14 0.15
HIGD2B ENST00000311755 83.56 98.36 93.83 0.30 0.21 0.10 0.52 0.14 0.13
NCBP2L ENST00000509000 94.36 98.80 98.94 0.10 0.16 0.10 0.11 0.14 0.04
FPR3 ENST00000339223 87.07 98.36 95.58 0.23 0.21 0.08 0.38 0.14 0.11
IFNA10 ENST00000357374 95.83 98.81 99.20 0.11 0.16 0.11 0.11 0.14 0.04
NAP1L6 ENST00000373518 99.34 98.37 99.99 0.11 0.21 0.13 0.12 0.14 0.04
AL079342.1 ENST00000369474 92.12 98.81 98.71 0.15 0.16 0.10 0.19 0.14 0.05
AL645730.2 ENST00000448346 91.31 98.37 97.75 0.15 0.21 0.09 0.20 0.14 0.04
MRPL36 ENST00000508987 96.48 98.82 99.36 0.10 0.16 0.11 0.11 0.14 0.04
ARHGEF35 ENST00000378115 95.04 98.38 98.84 0.10 0.21 0.10 0.12 0.14 0.05
KRTAP21-2 ENST00000333892 97.83 98.82 99.67 0.11 0.16 0.12 0.11 0.14 0.04
MAGEA6 ENST00000329342 94.86 98.38 98.79 0.10 0.21 0.10 0.11 0.14 0.05
TCEB3CL2 ENST00000591973 98.23 98.83 99.73 0.09 0.16 0.12 0.11 0.14 0.04
AC021860.1 ENST00000436901 91.36 98.39 98.17 0.15 0.21 0.09 0.20 0.14 0.05
USP17L2 ENST00000333796 95.80 98.83 99.18 0.11 0.16 0.11 0.11 0.14 0.04

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