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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
LRRC36 ENST00000329956 36.05 50.13 41.33 0.94 0.67 0.73 1.85 1.99 2.02
LPAR2 ENST00000542587 36.05 44.92 38.78 0.94 0.68 0.82 1.85 1.98 2.03
FAM124B ENST00000409685 51.00 72.47 62.65 0.61 0.47 0.51 1.85 1.03 1.40
CLEC3B ENST00000296130 51.01 71.39 61.93 0.61 0.53 0.48 1.85 1.05 1.45
GTF3C5 ENST00000372108 51.01 48.81 48.80 0.61 0.63 0.70 1.85 2.02 1.86
MPV17 ENST00000380044 51.02 88.51 72.45 0.61 0.23 0.44 1.85 0.36 0.83
HRASLS ENST00000264735 51.03 81.08 67.98 0.61 0.35 0.51 1.85 0.54 1.10
PRMT7 ENST00000339507 51.07 54.24 51.81 0.61 0.62 0.62 1.85 1.70 1.92
MCOLN2 ENST00000370608 51.07 67.35 59.49 0.61 0.56 0.49 1.85 1.21 1.70
MTFR1 ENST00000262146 51.08 74.08 63.87 0.61 0.53 0.49 1.85 1.03 1.39
CARD9 ENST00000371732 51.08 58.80 54.50 0.61 0.54 0.57 1.85 1.41 1.75
PAPL ENST00000331256 51.09 53.16 51.18 0.61 0.66 0.63 1.85 1.75 1.91
GPR116 ENST00000283296 51.09 18.54 32.97 0.61 1.49 0.86 1.85 0.76 1.67
CCDC77 ENST00000239830 51.11 70.43 61.47 0.61 0.52 0.44 1.85 1.08 1.48
PPP4R2 ENST00000356692 51.12 3.62 25.45 0.61 3.36 1.02 1.85 0.30 1.19
SH3BGRL2 ENST00000369838 51.12 94.14 75.61 0.61 0.25 0.38 1.85 0.25 0.64
ATP11A ENST00000487903 51.13 20.83 34.25 0.61 1.42 0.87 1.85 0.83 1.76
ZCCHC10 ENST00000324170 51.13 58.28 54.25 0.61 0.54 0.59 1.85 1.43 1.74
HOXC10 ENST00000303460 51.14 38.08 42.93 0.61 0.77 0.67 1.85 1.70 1.99
PLBD2 ENST00000280800 51.14 57.04 53.49 0.61 0.56 0.63 1.85 1.52 1.82
EMC9 ENST00000419198 51.15 63.94 57.48 0.61 0.48 0.52 1.85 1.21 1.65
DPY19L1 ENST00000310974 51.15 25.72 36.55 0.59 1.24 0.85 1.85 1.05 1.90
COA4 ENST00000355693 51.16 76.93 65.62 0.59 0.43 0.51 1.85 0.79 1.29
ZSWIM4 ENST00000254323 51.37 29.26 38.59 0.59 1.14 0.84 1.85 1.35 2.01
BBS4 ENST00000268057 51.38 64.01 57.66 0.59 0.48 0.51 1.85 1.20 1.67

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