Biomedical Engineering Reference
In-Depth Information
genomic data. Because of the massive quantity of data, investigators may
have diculty sorting through the information. Below, we describe an in-
tegrated bioinformatics tool to summarize the long list of genes into a few
concise tables which allow researchers to extract relevant biological func-
tions.
2.3.1. Integration of Genomic Databases
It is important to have a reliable database in order to yield more ac-
curate results of gene function classication. Our current database col-
lects major gene databases and integrates them into one more compre-
hensive database for classication. The database includes the Aymetrix
gene database
65
, NCBI Entrez database
66
, GO database
39
, and the KEGG
pathway database
67
. For example, the database in the Aymetrix's NetAx
Analysis Center contains detailed genomic information for each probe set
in Aymetrix gene chips. This information includes probe sequences, gene
annotations, and various functional annotations. However, it is not very in-
clusive, and some important gene variables are not available, such as gene
alias (gene synonym, a non-standard name for a gene) and gene RIF (ref-
erence into function). For gene alias, it is common to see multiple names
published for a particular gene. So, without the gene alias information, it is
dicult to recognize a set of dierent names for the same target gene. For
gene RIF, it gives a concise phrase (not a keyword) describing a gene func-
tion with a reference to a specic MEDLINE record. The phrase provides a
good opportunity to enhance gene classication. Accordingly, inclusion of
the gene alias and gene RIF with the Aymetrix's NetAx database will
undoubtedly make the data more valuable. Since the Entrez Gene database
includes biological information for genes but with limited probe informa-
tion for the Aymetrix gene chip, integration of these databases will make
gene function classication more accurate.
2.3.2. Systematic Layout of All Selected Genes
For a list of signicant genes, the integrated bioinformatics tool presents
a summary table to list the up- /down- regulated genes. Sorting the se-
lected genes into up- or down- regulation groups is a basic requirement
by biomedical researchers because an up-regulated gene has a dierent bi-
ological meaning compared to the same gene having a down-regulation.
To get detailed gene information, this summary table is linked to another
table where all up- (or down-) regulated genes are listed with their expres-
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