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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
MATN2 ENST00000520016 35.54 46.06 39.17 0.97 0.76 0.78 1.89 2.03 2.06
ZNF329 ENST00000598312 36.66 48.86 40.98 0.95 0.63 0.76 1.76 2.03 2.05
WDR17 ENST00000280190 38.28 45.89 40.35 0.92 0.75 0.80 1.73 2.03 2.01
TGM1 ENST00000206765 39.16 49.20 42.43 0.90 0.66 0.68 1.76 2.03 2.01
HGD ENST00000283871 42.40 49.06 44.19 0.76 0.67 0.62 1.75 2.03 2.05
TBCB ENST00000221855 43.08 48.86 44.51 0.82 0.65 0.61 1.77 2.03 2.04
NPC1L1 ENST00000289547 43.08 49.79 45.12 0.82 0.66 0.70 1.77 2.03 2.01
TIGD5 ENST00000504548 43.54 49.04 44.93 0.80 0.66 0.68 1.80 2.03 2.03
SDR9C7 ENST00000293502 43.78 49.50 45.35 0.75 0.65 0.70 1.78 2.03 1.99
SUCLG1 ENST00000393868 44.37 46.11 43.61 0.67 0.75 0.61 1.76 2.03 2.01
KARS ENST00000319410 45.10 49.21 45.85 0.63 0.66 0.68 1.75 2.03 1.97
ENTPD7 ENST00000370489 45.80 45.91 44.34 0.58 0.75 0.61 1.78 2.03 2.04
L3MBTL4 ENST00000284898 45.89 46.12 44.52 0.58 0.75 0.61 1.78 2.03 2.04
HOXD8 ENST00000313173 46.38 46.10 44.88 0.56 0.75 0.68 1.80 2.03 2.04
ARL9 ENST00000360096 47.00 46.07 45.21 0.56 0.76 0.70 1.81 2.03 2.00
ABCD4 ENST00000356924 48.16 49.57 47.70 0.56 0.66 0.65 1.78 2.03 1.89
C21orf91 ENST00000284881 48.37 46.03 45.90 0.56 0.77 0.70 1.80 2.03 1.98
TBC1D31 ENST00000287380 49.16 46.44 46.45 0.57 0.73 0.67 1.80 2.03 1.92
NT5C1B-RDH14 ENST00000532967 49.92 49.01 48.33 0.53 0.66 0.67 1.80 2.03 1.88
HFM1 ENST00000370425 50.42 49.77 48.97 0.57 0.66 0.71 1.81 2.03 1.84
MRPL45 ENST00000312513 50.81 49.05 48.83 0.59 0.67 0.70 1.83 2.03 1.85
GNMT ENST00000372808 51.66 46.23 47.77 0.58 0.73 0.65 1.85 2.03 1.88
NMNAT1 ENST00000377205 51.70 49.47 49.49 0.58 0.66 0.67 1.83 2.03 1.83
DCAF13 ENST00000297579 51.73 48.84 49.20 0.58 0.63 0.72 1.82 2.03 1.84
HHAT ENST00000545154 51.80 46.43 47.94 0.58 0.73 0.66 1.82 2.03 1.88

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