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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
RPL41 ENST00000546591 9.90 82.52 44.85 2.11 0.34 0.67 0.50 0.52 2.04
BAG2 ENST00000370693 17.35 62.91 38.43 1.47 0.51 0.84 0.87 1.31 2.04
VAMP1 ENST00000396308 19.02 62.70 39.24 1.58 0.51 0.78 0.95 1.31 2.04
FAM84B ENST00000304916 19.98 71.52 44.23 1.52 0.53 0.62 1.00 1.07 2.04
MED7 ENST00000286317 21.39 58.42 38.21 1.54 0.54 0.85 1.06 1.39 2.04
RHEBL1 ENST00000301068 21.44 70.92 44.79 1.56 0.49 0.66 1.07 1.07 2.04
TRPV4 ENST00000418703 21.98 57.96 38.28 1.51 0.56 0.85 1.03 1.46 2.04
DNAJC18 ENST00000302060 23.54 56.54 38.34 1.37 0.52 0.85 1.09 1.54 2.04
PIGC ENST00000367728 23.95 56.16 38.35 1.34 0.52 0.85 1.10 1.55 2.04
LHFPL2 ENST00000380345 25.08 55.09 38.38 1.38 0.57 0.84 1.15 1.63 2.04
VMA21 ENST00000330374 25.59 60.05 41.04 1.34 0.53 0.76 1.20 1.37 2.04
SMIM12 ENST00000521580 26.79 65.62 44.83 1.30 0.53 0.66 1.37 1.21 2.04
RPE ENST00000359429 26.88 65.46 44.78 1.30 0.53 0.66 1.36 1.25 2.04
TNNI1 ENST00000361379 26.96 65.42 44.82 1.30 0.53 0.66 1.36 1.25 2.04
TGM2 ENST00000361475 27.22 65.53 45.03 1.23 0.53 0.70 1.40 1.22 2.04
TNFAIP8 ENST00000504771 27.59 52.57 38.38 1.23 0.67 0.84 1.41 1.82 2.04
WDFY2 ENST00000298125 29.50 52.21 39.25 1.06 0.62 0.78 1.56 1.84 2.04
TACO1 ENST00000258975 29.84 52.39 39.46 1.05 0.62 0.77 1.60 1.82 2.04
RIMKLA ENST00000431473 29.96 55.85 41.11 1.08 0.51 0.76 1.59 1.58 2.04
LMBRD1 ENST00000370577 30.06 49.73 38.14 1.05 0.66 0.86 1.60 2.03 2.04
CDR2 ENST00000268383 30.81 55.06 41.12 0.96 0.58 0.76 1.63 1.63 2.04
UMPS ENST00000232607 30.96 50.92 39.32 0.97 0.63 0.80 1.66 1.94 2.04
C11orf68 ENST00000438576 32.26 49.48 39.26 0.96 0.66 0.78 1.70 2.03 2.04
S1PR3 ENST00000375846 32.46 59.52 44.53 0.96 0.51 0.62 1.70 1.41 2.04
SFRP4 ENST00000436072 32.58 52.96 40.99 0.96 0.63 0.76 1.70 1.78 2.04

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