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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
C17orf47 ENST00000321691 81.53 46.26 65.44 0.32 0.73 0.52 0.59 2.04 1.31
ANKRD24 ENST00000600132 86.70 46.21 68.44 0.24 0.73 0.47 0.40 2.04 1.06
FAM47E ENST00000424749 86.71 46.39 68.53 0.24 0.73 0.47 0.40 2.04 1.06
POLRMT ENST00000588649 86.81 49.19 70.25 0.24 0.66 0.43 0.40 2.04 0.91
FAM131C ENST00000375662 87.30 46.41 68.91 0.23 0.73 0.46 0.38 2.04 1.04
FAM184B ENST00000265018 87.33 46.18 68.78 0.23 0.73 0.46 0.38 2.04 1.06
CMTM6 ENST00000205636 96.91 49.11 76.02 0.09 0.66 0.38 0.11 2.04 0.62
NDP ENST00000378062 13.78 46.07 28.11 1.64 0.76 0.81 0.69 2.03 1.28
C3orf58 ENST00000315691 18.48 45.96 30.43 1.54 0.76 0.80 0.91 2.03 1.46
GLMN ENST00000370360 22.65 49.52 34.37 1.44 0.65 0.87 1.05 2.03 1.77
HRAS ENST00000451590 23.90 49.49 34.87 1.37 0.65 0.90 1.11 2.03 1.75
BTBD9 ENST00000481247 24.55 46.09 33.47 1.34 0.75 0.89 1.13 2.03 1.72
FAM20B ENST00000263733 26.74 49.06 36.01 1.30 0.67 0.87 1.35 2.03 1.79
DUSP3 ENST00000226004 28.96 48.87 37.18 1.10 0.63 0.81 1.53 2.03 1.97
PLA2G6 ENST00000332509 29.54 46.18 35.96 1.08 0.73 0.86 1.53 2.03 1.77
LMBRD1 ENST00000370577 30.06 49.73 38.14 1.05 0.66 0.86 1.60 2.03 2.04
HSCB ENST00000216027 31.23 49.27 38.54 0.97 0.65 0.84 1.68 2.03 2.02
C11orf68 ENST00000438576 32.26 49.48 39.26 0.96 0.66 0.78 1.70 2.03 2.04
CPT1B ENST00000360719 32.36 46.19 37.53 0.99 0.73 0.84 1.70 2.03 2.01
LRRC58 ENST00000295628 32.50 49.02 39.11 0.97 0.66 0.77 1.70 2.03 2.06
VSIG8 ENST00000368100 32.64 46.08 37.63 0.96 0.75 0.82 1.70 2.03 2.01
DAZAP2 ENST00000549555 33.03 46.02 37.75 0.94 0.77 0.84 1.71 2.03 2.01
KCNS3 ENST00000403915 33.85 49.55 40.04 0.91 0.66 0.82 1.73 2.03 1.98
RABGGTA ENST00000399409 34.88 46.03 38.71 0.94 0.77 0.82 1.84 2.03 2.02
TGIF1 ENST00000330513 35.33 49.75 40.70 0.92 0.66 0.81 1.87 2.03 2.05

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