This website provides a curated list of epigenetic machinery genes
(that is, genes encoding for epigenetic regulators) as described in
L Boukas, JM Havrilla, PF Hickey, AR Quinlan, HT Bjornsson, KD
Hansen.
Co-expression patterns define epigenetic regulators associated with
neurological dysfunction.
Genome Res 29: 532–542. (https://doi.org/10.1101/gr.239442.118)
Column Descriptions:
The columns are meant to provide information about basic properties of
each of the genes. They are the following:
- Gene Name
- pLI: A metric of loss-of-function intolerance
(initially derived by the ExAC consortium, now provided by gnomAD),
ranging between 0 and 1. The closer it is to 1, the more intolerant to
loss-of-function variation a gene is. Note that pLI is essentially a
binary measure.
- Coexprs: Co-expression status. In our paper we show
that epigenetic machinery genes can be partitioned into 3 categories:
‘highly co-expressed’, ‘co-expressed’, and ‘not co-expressed’, based on
their expression patterns in adult human tissues (GTEx). The genes in
the highly co-expressed category tend to have very high pLI scores, and
are enriched for genes causing neurodevelopmental Mendelian
disorders.
- Epigenetic Function: Whether the encoded protein is
a epigenetic writer, eraser, reader, remodeler, or dual function
regulator.
- Enzymatic activity: For writers, erasers, and
remodelers. For example, whether a writer enzyme is a histone
methyltransferase (HMT).
- Reader activity: For readers. For example, whether
a reader protein is a histone methylation reader (HMR).
- TF activity: Whether the encoded protein has a
DNA-binding domain classifying it as a TF as well.
- Chr: Chromosome
- gnomAD: Link to corresponding gnomAD entry
- OMIM: Link to corresponding OMIM entry
- GTEx: Link to corresponding GTEx entry
- COSMIC: Link to corresponding COSMIC entry
- UniProt: Link to corresponding UniProt entry
- Interpro: Link to corresponding Interpro entry