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GREAT

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calculates

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statistics

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by

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associating

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genomic

...

regions

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with

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nearby

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genes

...

and

...

applying

...

the

...

gene

...

annotations

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to

...

the

...

regions.

...

Association

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is

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a

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two

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step

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process.

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First,

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each

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gene

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is

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assigned

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a

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regulatory

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domain

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(i.e.

...

a

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genomic

...

range

...

wherein

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regulatory

...

elements

...

are

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likely

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to

...

target

...

to

...

the

...

gene).

...

Then,

...

a

...

genomic

...

region

...

is

...

associated

...

with

...

all

...

genes

...

whose

...

regulatory

...

region

...

it

...

overlaps.

...

How

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does

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GREAT

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define

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gene

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regulatory

...

domains?

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As

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of

...

yet,

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there

...

are

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no

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clear

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methods

...

for

...

identifying

...

the

...

regulatory

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domain

...

of

...

a

...

gene.

...

It

...

is

...

known

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that

...

regulatory

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elements

...

can

...

be

...

located

...

over

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one

...

million

...

bases

...

away

...

from

...

their

...

target

...

genes

...

and

...

even

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jump

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over

...

intervening

...

genes

...

Footnote Macro

...

lettice

...

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

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Shh

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enhancer

...

regulates

...

expression

...

in

...

the

...

developing

...

limb

...

and

...

fin

...

and

...

is

...

associated

...

with

...

preaxial

...

polydactyly.

...

Hum.

...

Mol.

...

Genet.

...

12

...

(14):1725-1735

...

(2003).

...

.

...

GREAT

...

allows

...

you

...

to

...

choose

...

from

...

among

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three

...

approaches

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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. When extending the regulatory domain of gene G beyond its basal domain, the extension to the "left" extends until it reaches the first basal domain of any gene whose transcription start site is "left" of G's transcription start site (and analogously for extending "right").

Image Added

Note: The methodology of extending beyond basal domains was slightly different in the previous GREAT v1.2 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.

Image Added

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.

Image Added

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
    Footnote Macro
    lettice
    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).

    • SHH: chr7:155438203-156584569
  • HOXD global control region
    Footnote Macro
    spitz
    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).

    • 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
    Footnote Macro
    levings
    levings

    Levings P.P., Bungert J. The human beta-globin locus control region. Eur. J. Biochem. 269(6):1589-1599 (2002).

    • HBB: chr11:5226931-5314124
    • HBD: chr11:5253302-5314124
    • HBG1: chr11:5260859-5314124
    • HBE1: chr11:5276088-5314124

Human (hg18)

  • Sonic hedgehog long-range enhancer
    Footnote Macro
    lettice
    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).

    • SHH: chr7:155130964-156277330
  • HOXD global control region
    Footnote Macro
    spitz
    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).

    • 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
    Footnote Macro
    levings
    levings

    Levings P.P., Bungert J. The human beta-globin locus control region. Eur. J. Biochem. 269(6):1589-1599 (2002).

    • HBB: chr11:5183507-5270700
    • HBG1: chr11:5209878-5270700
    • HBE1: chr11:5232664-5270700

Mouse (mm9)

  • Sonic hedgehog long-range enhancer
    Footnote Macro
    lettice
    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).

    • Shh: chr5:28644270-29642207
  • Hoxd global control region
    Footnote Macro
    spitz
    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).

    • 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
    Footnote Macro
    levings
    levings

    Levings P.P., Bungert J. The human beta-globin locus control region. Eur. J. Biochem. 269(6):1589-1599 (2002).

    • Hbb-b1 chr7:110945345-111023716
    • Hbb-b1 chr7:110967438-111023716
    • Hbb-bh1 chr7:110981442-111023716
    • Hbb-y chr7:110996677-111023716

References

Display Footnotes Macro
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