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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
SSX1 ENST00000376919 96.26 97.51 98.89 0.12 0.22 0.10 0.11 0.19 0.04
IDI2 ENST00000277517 97.93 95.82 98.89 0.11 0.22 0.10 0.11 0.20 0.04
C5orf56 ENST00000337752 99.26 94.55 98.90 0.11 0.23 0.10 0.12 0.24 0.04
PTTG2 ENST00000504686 94.32 99.36 98.91 0.10 0.16 0.10 0.11 0.12 0.04
EBLN2 ENST00000533473 96.15 97.63 98.91 0.11 0.22 0.10 0.11 0.20 0.04
IFNA14 ENST00000380222 95.84 98.13 98.92 0.11 0.20 0.10 0.11 0.16 0.04
C8orf17 ENST00000507535 93.95 99.79 98.92 0.11 0.17 0.10 0.13 0.11 0.04
MAGEA3 ENST00000393902 95.97 98.50 98.93 0.11 0.21 0.10 0.11 0.15 0.04
C8orf49 ENST00000525043 95.12 98.49 98.93 0.10 0.21 0.10 0.12 0.15 0.04
EID2B ENST00000326282 95.58 99.25 98.94 0.11 0.15 0.10 0.11 0.13 0.04
NCBP2L ENST00000509000 94.36 98.80 98.94 0.10 0.16 0.10 0.11 0.14 0.04
C16orf3 ENST00000408886 95.66 98.10 98.95 0.11 0.20 0.10 0.11 0.16 0.04
MTRNR2L10 ENST00000545075 94.01 99.82 98.95 0.10 0.17 0.10 0.13 0.11 0.04
SMIM21 ENST00000579022 98.67 95.29 98.96 0.10 0.23 0.10 0.11 0.21 0.04
TXNRD3NB ENST00000383572 97.47 96.51 98.96 0.10 0.22 0.10 0.11 0.19 0.04
IFNA2 ENST00000380206 94.77 99.71 98.97 0.10 0.17 0.10 0.11 0.11 0.04
H2AFB1 ENST00000354461 95.48 98.30 98.97 0.11 0.21 0.10 0.11 0.14 0.04
C2orf83 ENST00000264387 96.89 97.14 98.98 0.09 0.24 0.11 0.11 0.18 0.04
ZNF765 ENST00000396408 97.30 96.74 98.98 0.10 0.23 0.11 0.11 0.19 0.04
RP11-1070N10.3 ENST00000554161 94.12 99.89 98.99 0.10 0.17 0.11 0.13 0.11 0.04
OR2T34 ENST00000328782 96.46 97.56 98.99 0.10 0.22 0.11 0.11 0.19 0.04
CRIPAK ENST00000324803 95.70 98.22 99.00 0.11 0.21 0.11 0.12 0.15 0.04
RP11-863K10.7 ENST00000330539 94.14 99.90 99.00 0.10 0.17 0.11 0.13 0.10 0.04
FLG2 ENST00000388718 98.69 95.47 99.01 0.10 0.24 0.11 0.11 0.21 0.04
ZNF781 ENST00000358582 94.96 98.96 99.01 0.10 0.17 0.11 0.12 0.15 0.04

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