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The GLS Tool is a gene expression tool for a single cDNA library or a group of
libraries. First it finds all the expressed genes in the one or more libraries that
meet the chosen criteria of organism and library characteristics.
Then it "summarizes" or organizes these genes based on a selected field. Finally,
it classifies them into unique and non-unique, and known and unknown.
| What to Put In the Search Fields
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| Search Field
|
Options |
|
Organism |
Select "Homo sapiens" or "Mouse" from the drop down box. |
| Library Group |
There are three options:
- Keep the default setting of "CGAP Libraries" to search only CGAP libraries.
- Select MGC libraries
(The Mammalian Gene Collection).
- Select all EST libraries, which include both
subsets of CGAP and MGC libraries.
|
| Tissue Type |
Keep the default setting of "Any" to search all tissue types, or select
one specific tissue. |
| Tissue Preparation |
Keep the default setting "Any" that includes all library preparation methods
listed in
Tissue Preparation Overview, or choose one specific method.
|
| Tissue Histology |
Keep the default setting "Any" that includes normal, pre-cancerous, and cancer histology,
or select a specific histology. |
| Library Protocol |
Keep the default setting "Any" that includes all library protocol methods. The protocols
listed below the line are CGAP specific protocols described in
cDNA Library Protocols Overview.
|
| Library Name |
With all of the above settings at default, enter the exact
name of a CGAP or MGC library, e.g., NCI_CGAP_Pr1 or NIH_MGC_50.
|
| Summarize results by | Select one of the five criteria to
summarize the results based on this criterion. See "Summarizing the Results" below. |
Because of the many combinations of library criteria and result formats, the
investigator
can analyze tissues and libraries from many vantage points.
Below are a few examples:
- Select "prostate" and "cancer" to generate a list of unique genes
that may be potential markers for prostate cancer and
would be useful on a microarray.
- Select mouse and NCI_CGAP_Mam6 to find the unique genes in this one library.
- Compare the gene expression in "normalized" libraries from colon cancer with
"non-normalized" colon cancer - are there differences?
The expressed genes found by GLS may be "summarized" using five different criteria:
tissue, histology, tissue preparation, library protocol, and library name, each
of which takes the same pool of genes and places each unique and non-unique gene
in the appropriate, differently labeled "bin".
In the example below, the tool has summarized the human CGAP prostate
libraries each way as an example. Using UniGene Build 127, the
results appear as follows, summarized by:
a) Tissue
| Subset |
Libraries |
Sequences |
Unique Genes |
Non-Unique Genes |
|
|
|
Known | Unknown |
Known | Unknown |
| All prostate tissue | 19 | 69292 | 5 | 1017 | 6586 | 5423 |
| Prostate tissue | 19 | 69292
| 5 | 1017 | 6586 | 5423 |
b) Histology
c) Tissue preparation
d) Library protocol
e) Library name
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