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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
F8A1 ENST00000369446 71.56 99.59 88.75 0.38 0.16 0.20 0.82 0.12 0.28
MRPL36 ENST00000508987 96.48 98.82 99.36 0.10 0.16 0.11 0.11 0.14 0.04
AC020907.1 ENST00000313865 83.20 99.59 94.00 0.28 0.16 0.09 0.54 0.12 0.11
AL079342.1 ENST00000369474 92.12 98.81 98.71 0.15 0.16 0.10 0.19 0.14 0.05
FOXD4L6 ENST00000377473 93.47 99.58 96.63 0.13 0.16 0.08 0.15 0.12 0.08
IFNA10 ENST00000357374 95.83 98.81 99.20 0.11 0.16 0.11 0.11 0.14 0.04
NCBP2L ENST00000509000 94.36 98.80 98.94 0.10 0.16 0.10 0.11 0.14 0.04
MRGPRX1 ENST00000302797 96.36 99.58 99.49 0.10 0.16 0.11 0.11 0.12 0.05
LCE4A ENST00000368777 81.37 98.80 93.26 0.33 0.16 0.14 0.60 0.14 0.15
AL583828.1 ENST00000558378 97.88 99.57 99.52 0.11 0.16 0.12 0.11 0.12 0.05
IFNA13 ENST00000449498 95.54 98.79 99.11 0.11 0.16 0.11 0.11 0.14 0.04
CXorf67 ENST00000342995 99.08 99.57 99.72 0.11 0.16 0.12 0.12 0.12 0.04
AC107021.1 ENST00000422482 92.09 98.79 98.14 0.15 0.16 0.09 0.20 0.14 0.05
AC005477.1 ENST00000542853 93.42 99.56 98.50 0.13 0.16 0.10 0.15 0.12 0.05
OR14K1 ENST00000283225 99.61 98.78 99.94 0.12 0.16 0.13 0.13 0.14 0.04
TAS2R8 ENST00000240615 98.47 99.56 99.88 0.10 0.16 0.12 0.11 0.13 0.04
RFPL4B ENST00000441065 98.63 98.78 99.82 0.10 0.16 0.12 0.11 0.14 0.04
TAS2R10 ENST00000240619 88.56 99.55 96.89 0.20 0.16 0.08 0.34 0.13 0.07
OR8D1 ENST00000357821 95.24 98.77 98.88 0.10 0.16 0.10 0.11 0.14 0.04
NHLRC4 ENST00000424439 92.04 98.77 98.11 0.15 0.16 0.09 0.20 0.14 0.05
AC008132.13 ENST00000342005 93.39 99.55 97.57 0.13 0.16 0.09 0.15 0.13 0.06
NPIPA2 ENST00000553201 92.04 98.76 98.21 0.15 0.16 0.09 0.20 0.14 0.05
SRY ENST00000383070 93.37 99.54 97.44 0.15 0.16 0.08 0.15 0.13 0.07
KRTAP20-2 ENST00000330798 82.97 98.76 93.76 0.30 0.16 0.10 0.55 0.14 0.13
AC074389.6 ENST00000382528 97.95 99.54 99.80 0.11 0.16 0.12 0.11 0.13 0.04

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