Schema for Haploinsufficiency - Haploinsufficiency predictions for genes from DECIPHER
  Database: hg19    Primary Table: decipherHaploIns Data last updated: 2021-03-18
Big Bed File: /gbdb/hg19/bbi/haploins/haploinsufficiency.bb
Item Count: 19,124
Format description: Haploinsufficiency data in BED 9+2 format.
fieldexampledescription
chromchr1Chromosome (or contig, scaffold, etc.)
chromStart166808681Start position in chromosome
chromEnd166825581End position in chromosome
namePOGKName of item
score0Score from 0-1000
strand.+ or -
thickStart166808681Start of where display should be thick (start codon)
thickEnd166825581End of where display should be thick (stop codon)
itemRgb75,180,75RGB value for color of item
quantile62.23%Alpha-upper quantile of the predicted score (%HI)
prediction0.051341799Predicted score for haploinsufficiency of the item

Sample Rows
 
chromchromStartchromEndnamescorestrandthickStartthickEnditemRgbquantileprediction
chr1166808681166825581POGK0.16680868116682558175,180,7562.23%0.051341799
chr1166825747166845564TADA10.166825747166845564125,130,12543.82%0.144507777
chr1166882443166944719ILDR20.166882443166944719125,130,12545.59%0.132084602
chr1166958346166991451MAEL0.166958346166991451150,105,15037.16%0.196062632
chr1167022073167059868GPA330.16702207316705986825,230,2587.93%0.003404683
chr1167063282167098402DUSP270.16706328216709840250,205,5072.22%0.023951874
chr1167190066167396582POU2F10.167190066167396582255,0,2555.68%0.805592985
chr1167399877167487847CD2470.167399877167487847100,155,10055.28%0.079514711
chr1167498914167523004CREG10.16749891416752300450,205,5072.06%0.024343139
chr1167599330167675486RCSD10.16759933016767548625,230,2584.56%0.006023971

Haploinsufficiency (decipherHaploIns) Track Description
 

Description

This track displays haploinsufficiency predictions for human genes (Huang 2010). Human cells have two copies of most genes (one from each parent). If a mutation alters one copy, the other is usually still sufficient to maintain gene function. For haploinsufficient genes, however, both copies must be functioning for the organism to have a normal life. Haploinsufficiency is implicated in a number of health disorders.

Display Conventions

Predictions in this track are provided on a per-gene basis and are displayed in blocks corresponding to each gene's position in the genome (and labeled with that gene's name). The raw prediction scores range from 0 to 1, where 0 is very unlikely to be haploinsufficient and 1 is very likely. Because many of the predicted scores fall toward the lower end of the spectrum, the authors also grouped those scores by quantile. The quantile for each gene is shown as α-upper percentile, which shows the percentage of genes with a higher predicted score than this one. A gene with a relatively strong prediction of being haploinsufficient will have a quantile close to 0%. A gene with a very low comparative prediction of being haploinsufficient will have a quantile close to 100%.

Moving the mouse cursor over any gene will display a pop-up box with the gene name and α-upper quantile for the prediction. The genes in this track are also color-coded according to quantile:

  • Magenta shades indicate a higher expectation of being haploinsufficient
  • Green shades indicate a lower expectation of being haploinsufficient

Credits

Data for this track were generously provided by the DECIPHER project at https://decipher.sanger.ac.uk/about/downloads/data.

References

Huang N, Lee I, Marcotte EM, Hurles ME. Characterising and predicting haploinsufficiency in the human genome. PLoS Genet. 2010 Oct 14;6(10):e1001154. PMID: 20976243; PMC: PMC2954820