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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
AC007421.1 ENST00000593717 91.26 98.32 98.60 0.15 0.21 0.10 0.21 0.14 0.05
EBLN1 ENST00000422359 99.25 98.32 99.74 0.11 0.21 0.12 0.12 0.14 0.04
C5orf55 ENST00000408966 95.69 98.31 99.05 0.11 0.21 0.11 0.12 0.14 0.04
RBMXL3 ENST00000424776 88.54 98.31 96.27 0.20 0.21 0.07 0.34 0.14 0.09
H2AFB1 ENST00000354461 95.48 98.30 98.97 0.11 0.21 0.10 0.11 0.14 0.04
CTC-241N9.1 ENST00000499601 91.19 98.30 97.67 0.15 0.21 0.09 0.21 0.14 0.06
OCLM ENST00000574641 88.06 98.29 96.18 0.20 0.21 0.07 0.35 0.15 0.10
C9orf37 ENST00000371417 96.78 98.29 99.30 0.11 0.21 0.11 0.11 0.15 0.04
AC079341.1 ENST00000424958 91.18 98.28 97.65 0.15 0.21 0.09 0.21 0.15 0.06
OR5D16 ENST00000378396 86.54 98.27 95.25 0.25 0.21 0.08 0.41 0.15 0.10
AL353698.1 ENST00000433279 91.17 98.27 97.62 0.15 0.21 0.09 0.21 0.15 0.06
TMEM133 ENST00000303130 88.79 98.26 96.35 0.19 0.21 0.07 0.33 0.15 0.09
DHRS4-AS1 ENST00000354854 91.16 98.26 96.95 0.15 0.21 0.08 0.21 0.15 0.07
AC092811.1 ENST00000366845 91.15 98.25 97.61 0.15 0.21 0.09 0.21 0.15 0.06
OR4A15 ENST00000314706 94.86 98.25 98.72 0.10 0.21 0.10 0.11 0.15 0.05
MTRNR2L5 ENST00000512524 91.07 98.24 97.54 0.16 0.21 0.08 0.21 0.15 0.07
AF131215.5 ENST00000400102 91.06 98.24 98.42 0.16 0.21 0.10 0.21 0.15 0.05
AC019294.1 ENST00000543887 91.01 98.23 97.54 0.16 0.21 0.08 0.21 0.15 0.07
RP11-382J12.1 ENST00000499227 90.99 98.23 97.52 0.16 0.21 0.08 0.21 0.15 0.07
VN1R1 ENST00000321039 99.87 98.22 99.90 0.12 0.21 0.12 0.14 0.15 0.04
CRIPAK ENST00000324803 95.70 98.22 99.00 0.11 0.21 0.11 0.12 0.15 0.04
FLJ45079 ENST00000374983 98.97 98.21 99.77 0.10 0.21 0.12 0.12 0.15 0.04
CEMP1 ENST00000382350 97.80 98.21 99.54 0.11 0.20 0.12 0.11 0.15 0.05
AC025278.1 ENST00000377296 90.95 98.20 97.08 0.16 0.20 0.08 0.21 0.15 0.07
KRTAP19-8 ENST00000382822 85.90 98.20 94.87 0.27 0.20 0.09 0.45 0.15 0.11

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