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Gene Expression and Vocabularies

Win Hide winhide at sanbi.ac.za
Thu Feb 15 23:09:35 PST 2001


Dear Fritz;

Following up on Judy and Mike's responses, I'd like to mention that
there is a a recognised need for 'expression ontologies' that can
encompass the isoforms of each gene expression product, and relate this
isoform to the expression state in which it was captured.

That said, clearly, the capture of expression state itself needs to have
a standardised vocabulary at the very least. This is an effort, that in
collaboration with Chris Stoekert's group at CBIL and Mark McCarthy's
Group at Imperial College, London, we are endeavouring to perform, using
standardised terms for the expression captures of EST libraries. 

But how to describe expression product variation itself? This problem I
am attempting to organise in terms of an exon expression
language/vocabulary. ExScript. As a very basic start the language will
result from the following:


A mature transcription product is made up of transcribed DNA that has
been spliced to result in exons in a certain order. The position of a
transcription initiation start site, a poly adenylation signal or a
splice site signal and (perhaps) its strength, defines the boundary of
an exon within a gene. The combined set of boundary co-ordinates for
each transcript thus defines the final mature transcription product.

A language that defines the message must satisfy several criteria if it
is to provide an adequate description.

The boundary co-ordinate set (string) must provide machine and human
readable information on the expression product, whether directly, or
indirectly through its unique association with a record of expression.
The boundary co-ordinate description must provide:

A unique association with the combined exon product
A relative or non-relative description of each exon's position
The total number of exons
The length of each exon in nucleotides
The total length of the mature transcript
The relative expression of each exon
The the start and stop position of each exon - relative to the parent
gene
Endedness of each exon trunctation or extension
Weather an exon does or does not code for amino acids
The reading frame for each expression form of amino acids.

I am writing this up for an editorial for 'Bioinformatics', and will
make the specifications, as they develop, open to this group. I seek
input from this group to provide some grounded inputs..

Thank you for nudging this question into our awareness.

Win

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