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GREAT calculates statistics by associating genomic regions with nearby genes and applying the gene annotations to the regions. Association is a two step process. First, each gene is assigned a regulatory domain (i.e. a genomic range wherein regulatory elements are likely to target to the gene). Then, a genomic region is associated with all genes whose regulatory region it overlaps.

How does GREAT define gene regulatory domains?

As of yet, there are no clear methods for identifying the regulatory domain of a gene. It is known that regulatory elements can be located over one million bases away from their target genes and even jump over intervening genes<ref name="lettice">Lettice L.A., Heaney S.J., Purdie L.A., Li L., de Beer P., Oostra B.A., Goode D., Elgar G., Hill R.E., de Graaff E. A long-range Shh enhancer regulates expression in the developing limb and fin and is associated with preaxial polydactyly. Hum. Mol. Genet. 12(14):1725-1735 (2003).1

    • SHH: chr7:155438203-156584569
  • HOXD global control region<ref name="spitz">Spitz F., Gonzalez F., Dubuole D. A global control region defines a chromosomal regulatory landscape containing the HoxD cluster. Cell 113(3):405-417 (2003).2
    • HBB: chr11:5226931-5314124
    • HBD: chr11:5253302-5314124
    • HBG1: chr11:5260859-5314124
    • HBE1: chr11:5276088-5314124

Human (hg18)

  • Sonic hedgehog long-range enhancer<ref name="lettice">Lettice L.A., Heaney S.J., Purdie L.A., Li L., de Beer P., Oostra B.A., Goode D., Elgar G., Hill R.E., de Graaff E. A long-range Shh enhancer regulates expression in the developing limb and fin and is associated with preaxial polydactyly. Hum. Mol. Genet. 12(14):1725-1735 (2003).3
    • LNP: chr2:176423101-176655936
    • EVX2: chr2:176423101-176661936
    • HOXD13: chr2:176423101-176667775
    • HOXD12: chr2:176423101-176675329
    • HOXD11: chr2:176423101-176684737
    • HOXD10: chr2:176423101-176690737
  • Beta-globin locus control region<ref name="levings">Levings P.P., Bungert J. The human beta-globin locus control region. Eur. J. Biochem. 269(6):1589-1599 (2002).4
    • Shh: chr5:28644270-29642207
  • Hoxd global control region<ref name="spitz">Spitz F., Gonzalez F., Dubuole D. A global control region defines a chromosomal regulatory landscape containing the HoxD cluster. Cell 113(3):405-417 (2003).5
    • Hbb-b1 chr7:110945345-111023716
    • Hbb-b1 chr7:110967438-111023716
    • Hbb-bh1 chr7:110981442-111023716
    • Hbb-y chr7:110996677-111023716

References

Footnotes
Ref Notes
1

. GREAT allows you to choose from among three approaches to defining gene regulatory domains.

Note that GREAT measures all distances from the transcription start site of a gene's canonical isoform.

Approach 1: Basal plus extension

Each gene is assigned a basal regulatory domain of a minimum distance upstream and downstream of the TSS (regardless of other nearby genes). The gene regulatory domain is extended in both directions to the nearest gene's basal domain but no more than a maximum extension in one direction.

Note: This association rule has been modified slightly in the GREAT v1.5 release.

Approach 2: Two nearest genes

Each gene is assigned a regulatory domain that extends in both directions to the nearest gene's TSS but no more than a maximum extension in one direction.

Approach 3: Single nearest gene

Each gene is assigned a regulatory domain that extends in both directions to the midpoint between the gene's TSS and the nearest gene's TSS but no more than a maximum extension in one direction. This has the effect of assigning a region to the single nearest gene.

All three of the regulatory domain assignment rules are based on a unique ordering of the loci within the genome. However, there are a few distinct loci that possess identical canonical TSS positions. GREAT breaks ties in TSS positions using the arbitrary comparison of strand (+ first) and then the UCSC ID of the gene.

Curated Regulatory Domains

In addition to the above association rules, GREAT utilizes a set of literature curated regulatory domains. Where experimental evidence demonstrates that a gene is directly regulated by an element that falls outside of its putative regulatory domain (as defined by the default Basal plus extension rule), GREAT includes a curated regulatory domain that extends the regulatory domain for the gene to include its known regulatory element. The curated regulatory domains override the automatic rules. To ignore the curated regulatory domains, uncheck the option to "Include curated regulatory domains" in the Association rule settings area of the input screen.

Currently, the curated regulatory domains are:

Human (hg19)

  • Sonic hedgehog long-range enhancer<ref name="lettice">Lettice L.A., Heaney S.J., Purdie L.A., Li L., de Beer P., Oostra B.A., Goode D., Elgar G., Hill R.E., de Graaff E. A long-range Shh enhancer regulates expression in the developing limb and fin and is associated with preaxial polydactyly. Hum. Mol. Genet. 12(14):1725-1735 (2003).
2
    • LNP: chr2:176714855-176947690
    • EVX2: chr2:176714855-176953690
    • HOXD13: chr2:176714855-176959529
    • HOXD12: chr2:176714855-176967083
    • HOXD11: chr2:176714855-176976491
    • HOXD10: chr2:176714855-176982491
  • Beta-globin locus control region<ref name="levings">Levings P.P., Bungert J. The human beta-globin locus control region. Eur. J. Biochem. 269(6):1589-1599 (2002).
3
    • SHH: chr7:155130964-156277330
  • HOXD global control region<ref name="spitz">Spitz F., Gonzalez F., Dubuole D. A global control region defines a chromosomal regulatory landscape containing the HoxD cluster. Cell 113(3):405-417 (2003).
4
    • HBB: chr11:5183507-5270700
    • HBG1: chr11:5209878-5270700
    • HBE1: chr11:5232664-5270700

Mouse (mm9)

  • Sonic hedgehog long-range enhancer<ref name="lettice">Lettice L.A., Heaney S.J., Purdie L.A., Li L., de Beer P., Oostra B.A., Goode D., Elgar G., Hill R.E., de Graaff E. A long-range Shh enhancer regulates expression in the developing limb and fin and is associated with preaxial polydactyly. Hum. Mol. Genet. 12(14):1725-1735 (2003).
5
    • Lnp chr2:73770001-74496641
    • Evx2 chr2:74284768-74502220
    • Hoxd13 chr2:74284768-74508266
    • Hoxd12 chr2:74284768-74515449
    • Hoxd11 chr2:74284768-74525027
    • Hoxd10 chr2:74284768-74531027
  • Beta-globin locus control region<ref name="levings">Levings P.P., Bungert J. The human beta-globin locus control region. Eur. J. Biochem. 269(6):1589-1599 (2002).
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