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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
NLRP4 ENST00000301295 99.35 40.95 72.91 0.11 0.61 0.40 0.12 1.79 0.81
MRGPRX4 ENST00000314254 99.35 98.69 99.91 0.11 0.18 0.12 0.12 0.15 0.04
NAP1L6 ENST00000373518 99.34 98.37 99.99 0.11 0.21 0.13 0.12 0.14 0.04
ZSCAN5A ENST00000587340 99.34 53.70 79.84 0.11 0.63 0.37 0.12 1.69 0.52
LILRA5 ENST00000301219 99.33 81.09 92.95 0.11 0.35 0.14 0.12 0.55 0.15
APOL2 ENST00000249066 99.33 90.08 97.35 0.11 0.25 0.08 0.12 0.37 0.07
TRIM64C ENST00000530230 99.32 83.76 94.31 0.11 0.28 0.10 0.12 0.47 0.12
ZNF562 ENST00000448622 99.32 60.85 83.43 0.11 0.56 0.33 0.12 1.41 0.40
ZNF284 ENST00000421176 99.31 91.26 97.83 0.11 0.23 0.09 0.12 0.34 0.04
C17orf77 ENST00000392620 99.31 98.33 99.86 0.11 0.21 0.12 0.12 0.14 0.04
MUC6 ENST00000421673 99.30 49.47 77.60 0.11 0.66 0.37 0.12 2.02 0.56
TNFRSF10A ENST00000221132 99.30 80.06 92.36 0.11 0.37 0.14 0.12 0.60 0.15
AL603965.1 ENST00000335083 99.29 99.79 99.96 0.11 0.17 0.13 0.12 0.11 0.04
PROL1 ENST00000399575 99.29 88.72 96.81 0.11 0.27 0.08 0.12 0.35 0.07
GIMAP8 ENST00000307271 99.28 55.74 80.82 0.11 0.52 0.39 0.12 1.59 0.51
APOBEC3B ENST00000333467 99.28 73.38 89.45 0.11 0.54 0.18 0.12 1.03 0.24
APOBEC3D ENST00000216099 99.27 86.40 95.61 0.11 0.25 0.08 0.12 0.42 0.11
SPANXN2 ENST00000370498 99.27 94.08 98.73 0.11 0.25 0.10 0.12 0.26 0.05
C5orf56 ENST00000337752 99.26 94.55 98.90 0.11 0.23 0.10 0.12 0.24 0.04
FAM24A ENST00000368894 99.26 95.67 99.23 0.11 0.23 0.11 0.12 0.20 0.04
EBLN1 ENST00000422359 99.25 98.32 99.74 0.11 0.21 0.12 0.12 0.14 0.04
C11orf45 ENST00000310799 99.25 88.36 96.59 0.11 0.23 0.08 0.12 0.37 0.07
RAET1E ENST00000357183 99.24 84.26 94.48 0.11 0.28 0.10 0.12 0.44 0.12
DEFB125 ENST00000382410 99.24 95.82 99.26 0.11 0.22 0.11 0.12 0.20 0.04
CCL23 ENST00000293280 99.23 86.00 95.35 0.11 0.27 0.08 0.12 0.43 0.10

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