Web document 16.4. Definitions of
functional elements from the Oreganno database (www.oreganno.org).
Source: http://www.oreganno.org/oregano/help/records.html
“ORegAnno allows the annotation of several record types.
More can be added, any can be altered on discussion with the ORegAnno mailing
list (see Mailing
Lists)
- Regulatory Region:
A regulatory region is a noncoding DNA sequence that is known to alter the
expression of a particular gene. Canonical examples of regulatory regions
are promoters and enhancers.
- Transcription Factor:
A transcription factor record is a noncoding DNA sequence that is bound by
a particular transcription factor in vivo to alter the expression of a
particular gene. An example might be an experimentally confirmed Sp1
binding site.
- Regulatory
Polymorphism: A regulatory polymorphism record is a noncoding DNA
sequence that may or may not be bound by a known transcription factor in
vivo, but has an allelic variant that is confirmed to alter the expression
of a particular gene. An example might be an experimentally confirmed Sp1
binding site that has two allelic variants, one of which, when present,
downregulates its target gene (like MDM2, see Bond et al., Cell. 2004). Another
example may be an allele in a non-coding region which is confirmed to
alter expression patterns through a transcript quantification assay.
- Regulatory Haplotype:
A regulatory haplotype record is a noncoding DNA sequence that contains
many alleles in linkage disequilibrium (LD) that are confirmed to alter
the expression of a particular gene. This is different than a regulatory
polymorphism as the specific causal variant may not be known,
only the alleles that are in LD with it.”