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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
MAP3K2 ENST00000409947 11.59 0.96 3.67 1.73 4.10 3.83 0.59 0.29 0.23
HNRNPK ENST00000376263 0.91 0.96 0.13 4.35 4.08 4.86 0.18 0.29 0.18
STAT3 ENST00000264657 1.22 0.95 0.20 4.39 4.08 4.87 0.17 0.29 0.18
ZNF777 ENST00000247930 5.16 0.95 1.20 3.44 4.09 4.43 0.31 0.29 0.21
NSD1 ENST00000439151 3.50 0.94 0.73 3.83 4.09 4.60 0.30 0.29 0.20
MED14 ENST00000324817 14.13 0.93 4.79 1.62 4.10 3.67 0.71 0.29 0.24
DAAM2 ENST00000398904 31.52 0.93 13.91 0.95 4.10 2.09 1.69 0.29 0.59
HNRNPM ENST00000325495 15.98 0.92 5.68 1.53 4.10 3.34 0.79 0.29 0.27
NCBP1 ENST00000375147 3.85 0.92 0.79 3.77 4.11 4.55 0.30 0.29 0.21
PIAS1 ENST00000249636 10.93 0.91 3.38 1.90 4.09 3.88 0.57 0.29 0.23
TCF20 ENST00000359486 28.11 0.91 12.07 1.16 4.09 2.29 1.48 0.29 0.48
STAG2 ENST00000218089 4.70 0.90 1.04 3.63 4.07 4.44 0.31 0.29 0.21
KPNB1 ENST00000290158 0.54 0.90 0.08 4.39 4.08 4.86 0.19 0.29 0.15
USP34 ENST00000398571 11.05 0.89 3.41 1.85 4.08 3.87 0.59 0.29 0.23
DNAJC14 ENST00000357606 17.28 0.89 6.39 1.46 4.08 3.06 0.88 0.29 0.32
ZNF407 ENST00000299687 46.12 0.88 21.66 0.58 4.09 1.27 1.81 0.29 0.91
SATB2 ENST00000417098 0.61 0.88 0.09 4.36 4.09 4.88 0.19 0.29 0.15
NF2 ENST00000338641 7.48 0.87 1.97 2.77 4.10 4.12 0.39 0.29 0.24
KIF11 ENST00000260731 1.88 0.87 0.29 4.27 4.10 4.86 0.24 0.29 0.18
ANKRD52 ENST00000267116 5.90 0.86 1.42 3.13 4.10 4.34 0.33 0.29 0.23
PREX1 ENST00000371941 16.14 0.86 5.74 1.51 4.11 3.30 0.80 0.29 0.28
LUC7L3 ENST00000505658 1.17 0.85 0.14 4.39 4.11 4.85 0.17 0.28 0.18
TM9SF3 ENST00000371142 2.62 0.85 0.46 4.02 4.11 4.75 0.28 0.28 0.17
ZDHHC5 ENST00000287169 22.78 0.84 9.28 1.43 4.10 2.32 1.06 0.28 0.38
KIF5C ENST00000435030 8.24 0.84 2.21 2.54 4.08 4.08 0.43 0.28 0.23

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