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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
C12orf74 ENST00000397833 94.78 93.06 96.71 0.10 0.28 0.08 0.11 0.30 0.08
C6orf118 ENST00000230301 94.79 86.92 93.62 0.10 0.22 0.13 0.11 0.41 0.15
KIR2DL4 ENST00000345540 94.79 67.44 84.46 0.10 0.54 0.33 0.11 1.20 0.40
PRLH ENST00000165524 94.80 93.04 96.72 0.10 0.28 0.08 0.11 0.30 0.08
S100A7L2 ENST00000368725 94.80 67.69 84.59 0.10 0.53 0.34 0.11 1.19 0.40
IQCF5 ENST00000446461 94.81 62.92 82.23 0.10 0.51 0.35 0.11 1.31 0.44
OR5H6 ENST00000383696 94.81 92.26 96.28 0.10 0.25 0.07 0.11 0.30 0.09
ERVMER34-1 ENST00000443173 94.82 98.58 98.84 0.10 0.20 0.10 0.11 0.15 0.05
GDF15 ENST00000252809 94.82 92.52 96.45 0.10 0.29 0.07 0.11 0.31 0.09
ZNF497 ENST00000311044 94.83 99.49 99.09 0.10 0.16 0.11 0.11 0.13 0.04
SIGLEC10 ENST00000356298 94.83 34.47 66.34 0.10 0.80 0.53 0.11 1.55 1.20
ZNF229 ENST00000588931 94.84 86.34 93.29 0.10 0.25 0.13 0.11 0.43 0.15
CT45A5 ENST00000463085 94.85 97.35 98.38 0.10 0.23 0.10 0.11 0.19 0.05
S100A12 ENST00000368737 94.85 76.27 88.70 0.10 0.44 0.20 0.11 0.86 0.28
MAGEA6 ENST00000329342 94.86 98.38 98.79 0.10 0.21 0.10 0.11 0.14 0.05
OR4A15 ENST00000314706 94.86 98.25 98.72 0.10 0.21 0.10 0.11 0.15 0.05
SLC17A1 ENST00000244527 94.87 72.69 86.98 0.10 0.47 0.28 0.11 1.04 0.30
KHDC1L ENST00000370388 94.87 75.68 88.40 0.10 0.44 0.22 0.11 0.90 0.30
H1FNT ENST00000335017 94.88 98.92 98.78 0.10 0.17 0.10 0.11 0.15 0.05
IGFN1 ENST00000335211 94.88 51.61 76.35 0.10 0.62 0.35 0.11 1.87 0.61
PSG2 ENST00000406487 94.89 97.45 98.43 0.10 0.22 0.10 0.12 0.19 0.05
NOBOX ENST00000467773 94.89 40.60 69.98 0.10 0.63 0.47 0.12 1.77 0.92
ZNF729 ENST00000601693 94.90 52.15 76.62 0.10 0.62 0.37 0.12 1.85 0.61
DSCR4 ENST00000328264 94.90 94.81 97.48 0.10 0.23 0.08 0.12 0.24 0.07
CD200R1 ENST00000308611 94.91 74.03 87.61 0.10 0.53 0.25 0.12 1.03 0.31

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