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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
ANXA2R ENST00000314890 99.85 98.39 100.00 0.12 0.21 0.13 0.13 0.14 0.04
CXorf27 ENST00000341016 99.56 99.69 99.99 0.12 0.17 0.13 0.13 0.11 0.04
NAP1L6 ENST00000373518 99.34 98.37 99.99 0.11 0.21 0.13 0.12 0.14 0.04
TCEB3CL ENST00000451265 99.93 99.20 99.98 0.10 0.15 0.13 0.14 0.13 0.04
MAS1L ENST00000377127 99.39 99.83 99.98 0.11 0.17 0.13 0.12 0.11 0.04
FLJ14816 ENST00000593290 99.14 99.73 99.97 0.11 0.17 0.13 0.12 0.11 0.04
OR2AK2 ENST00000366480 99.70 98.98 99.97 0.12 0.17 0.13 0.13 0.15 0.04
AL359878.1 ENST00000381466 99.71 98.92 99.96 0.12 0.17 0.13 0.13 0.15 0.04
AL603965.1 ENST00000335083 99.29 99.79 99.96 0.11 0.17 0.13 0.12 0.11 0.04
SMCP ENST00000368765 99.47 99.18 99.95 0.11 0.15 0.13 0.13 0.14 0.04
ARIH2OS ENST00000408959 98.82 99.81 99.95 0.10 0.17 0.13 0.11 0.11 0.04
OR14K1 ENST00000283225 99.61 98.78 99.94 0.12 0.16 0.13 0.13 0.14 0.04
OR7G3 ENST00000305444 98.80 99.70 99.94 0.10 0.17 0.12 0.11 0.11 0.04
TCEB3C ENST00000330682 99.99 99.68 99.93 0.10 0.17 0.12 0.14 0.11 0.04
C10orf111 ENST00000378207 98.82 99.50 99.93 0.10 0.16 0.12 0.11 0.13 0.04
C6orf195 ENST00000296847 98.56 99.71 99.92 0.10 0.17 0.12 0.11 0.11 0.04
RNASE2 ENST00000304625 99.66 98.41 99.92 0.12 0.21 0.12 0.13 0.14 0.04
TAS2R46 ENST00000533467 99.40 98.63 99.91 0.11 0.20 0.12 0.12 0.15 0.04
MRGPRX4 ENST00000314254 99.35 98.69 99.91 0.11 0.18 0.12 0.12 0.15 0.04
VN1R1 ENST00000321039 99.87 98.22 99.90 0.12 0.21 0.12 0.14 0.15 0.04
PRR23A ENST00000383163 98.19 99.96 99.90 0.11 0.18 0.12 0.11 0.09 0.04
C11orf72 ENST00000333139 99.92 99.44 99.89 0.10 0.16 0.12 0.14 0.12 0.04
MRGPRX2 ENST00000329773 98.74 99.21 99.89 0.10 0.15 0.12 0.11 0.13 0.04
TAS2R8 ENST00000240615 98.47 99.56 99.88 0.10 0.16 0.12 0.11 0.13 0.04
NPAP1 ENST00000329468 99.37 99.40 99.88 0.11 0.16 0.12 0.12 0.12 0.04

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