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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
ZNF367 ENST00000375256 1.39 18.27 7.22 4.32 1.48 2.81 0.19 0.74 0.34
GABPB1 ENST00000220429 1.43 12.85 4.42 4.31 2.07 3.72 0.20 0.59 0.25
KAT7 ENST00000259021 1.46 2.06 0.49 4.31 3.71 4.73 0.21 0.29 0.17
SNRPC ENST00000244520 1.49 28.32 12.45 4.31 1.16 2.23 0.20 1.22 0.50
BCL2L2-PABPN1 ENST00000557008 1.40 26.95 11.78 4.31 1.23 2.21 0.19 1.12 0.46
MAPK8 ENST00000374189 1.43 6.23 1.70 4.31 2.73 4.25 0.20 0.36 0.23
RAP1A ENST00000369709 1.46 27.94 12.30 4.31 1.20 2.25 0.21 1.19 0.50
CAND1 ENST00000545606 1.67 1.18 0.33 4.31 4.01 4.82 0.22 0.28 0.18
SMU1 ENST00000397149 1.49 1.36 0.33 4.31 3.96 4.83 0.20 0.27 0.18
PRMT8 ENST00000382622 1.40 7.31 2.10 4.31 2.57 4.10 0.20 0.37 0.23
POU3F2 ENST00000328345 1.44 17.55 6.84 4.31 1.58 2.94 0.21 0.72 0.33
AKT3 ENST00000366539 1.47 4.58 1.18 4.31 3.24 4.42 0.20 0.32 0.21
TXNL4A ENST00000269601 1.67 90.41 44.57 4.31 0.25 0.62 0.22 0.37 2.05
TBL1XR1 ENST00000430069 1.50 1.41 0.34 4.31 3.95 4.81 0.20 0.27 0.18
FEZF2 ENST00000283268 1.41 7.72 2.26 4.31 2.53 4.06 0.20 0.43 0.23
FOXJ3 ENST00000372572 1.70 10.07 3.33 4.30 2.33 3.89 0.22 0.49 0.23
RALA ENST00000005257 1.62 10.04 3.26 4.30 2.35 3.88 0.20 0.49 0.24
CNOT1 ENST00000317147 1.74 0.01 0.11 4.30 4.12 4.88 0.22 0.26 0.17
RPS3 ENST00000278572 1.47 18.58 7.40 4.30 1.49 2.80 0.20 0.76 0.34
NOTCH2NL ENST00000369340 1.68 37.89 17.70 4.30 0.80 1.67 0.22 1.70 0.78
PTP4A2 ENST00000344035 1.50 13.23 4.70 4.30 2.05 3.68 0.20 0.60 0.25
GSPT1 ENST00000434724 1.71 3.43 0.89 4.30 3.41 4.49 0.22 0.29 0.21
UBA2 ENST00000246548 1.62 2.92 0.75 4.30 3.49 4.58 0.21 0.29 0.20
USP7 ENST00000344836 1.74 0.31 0.15 4.30 4.12 4.84 0.22 0.29 0.18
RPL38 ENST00000311111 1.48 28.97 12.77 4.30 1.15 2.11 0.20 1.31 0.52

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