Gene-order map: explanation of the format
----------------------------------------The gene-order map communicates both gene order and cytological location.
This is presentationally rather different on a genome-wide map than on a
small, well-mapped region, and a novel format has been adopted, which is
documented here.
1. Cytological range
Each gene whose cytological location is known with a range of uncertainty
less than about two number divisions is written on a vertical line whose
extent is the range of uncertainty. Overlapping lines are staggered. To
this extent, in other words, the format is as in the EofD. A gene whose
symbol exceeds nine characters may cross more than one line; the line it
is attached to always goes through the second character of the symbol.
Bands are drawn with differing sizes, but this is not in any way related
to amount of DNA per band, as it is on the EofD. It is only a function
of
how much data we need to place there.
2. "Limiting" genes
In addition, at either end of the line there is the symbol for a gene
that
is known to lie to the indicated side of the gene in the middle of the
line. Two points must be emphasised about these "limiting" genes: they
are not being stated to have the same cytological location as the
"limited"
gene, and they are not being stated definitely to be the neighbouring
gene. They are chosen by pragmatic criteria as being the most
informative
genes that are known to lie to the indicated side. These criteria
include
cytological location and size of range of uncertainty of that location.
This means that it is common, especially in well-mapped regions, for a
gene
to appear more than once. A gene can appear as a limiter of any number
of
other genes, but it will only be a limited gene on at most one line.
Limiters are identified only by direct recombination, complementation or
molecular map data; cytology (of genes or of breakpoints) is never used.
If a gene has no limiter on one side (or both), that means that no gene
can be placed to that side using direct genetic or molecular data.
3. Multiple "limited" genes on a single line
In the better-characterised regions, gene order is known to a degree that
cannot be clearly represented by cytological range. This is alleviated
by placing two or more genes "limited" on the same line. So as to
maintain
completeness of information, a set of genes is only ever limited on the
same line if (a) their relative order is completely known, and (b) they
all have identical cytological ranges. The limiters of a line with more
than one gene are known to lie to the indicated side of all limited
genes.
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1B5
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1B6
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y
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svr
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elav
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Appl
This says:
- the four genes shown are in the order y, svr, elav, Appl,
going from left to right along the chromosome.
- svr and elav lie in either 1B5 or 1B6.
It does not say:
- y and/or Appl lie in 1B5 or 1B6
- svr lies in 1B5
etc.
4. Nested or overlapping genes
The software that analyses map data understands the concept of genes
within
genes, but this is hard to depict graphically without a generally more
confusing format. Sometimes, therefore, a gene will be shown as its own
limiter, or as both limited by and limiting (to the same side) another
gene.
We have incorporated some molecular data into this map, and will add much
more over the coming year, but the bulk of the information is based on
genetic data. Therefore, the definition of overlap of two genes is not
necessarily that the transcription units overlap. For example, ftz is
shown as embedded in Scr, because Scr[-] ftz[+] deficiencies exist that
delete proximal material (including Antp).
5. Genes with cytological extent
A few dozen genes are stated to be deleted by deficiencies which
(according
to our data) do not quite overlap, thus implying that the gene occupies
the
whole region between the deficiencies (plus a bit on either side). In
most
cases the gap between the genes is only one band, so we have fudged the
issue by placing the gene at the interband, eg y in 1B1-2:
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1B1
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1B2
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y
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ac
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sc
arth
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y
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ac