The Digital Gene Expression Displayer analyzes the differences in
gene expression between two pools of libraries. Unlike the cDNA xProfiler, which lists
every gene (even if an EST is seen only once in a pool) in both groups,
the DGED
finds only the statistically significant
differences, based on the sequence odds ratio and
a Bayesian test .
What to Put in the Query Fields |
The initial selection of library pools A and B is similar
to the cDNA xProfiler.
Query Field
|
Options |
1. Organism |
Select "Homo sapiens" or "Mouse" from the drop down box. |
2. Library Group |
There are three options:
- Keep the default setting of "All EST Libraries" to search all cDNA libraries in dbEST.
- Select MGC libraries
(The Mammalian Gene Collection) or
CGAP libraries or
ORESTES libraries.
- Select any grouping of MGC, CGAP, and ORESTES.
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3. Minimum sequences |
The minimum number of sequences
per cDNA library is set to 1000 by default.
However, a user may enter a lower minimum number to include libraries
of interest with the understanding the significance of the results may be lowered.
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4. List libraries by | Select any option to organize the
list of libraries for review on the set-up page.
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5. Pools A and B | |
i) Tissue Type |
There are 4 options:
- The default setting is all tissues (nothing is highlighted)
with the "Include" button selected. This searches all tissue types.
- Keep the default setting of all tissues, check "Exclude", and
highlight one or more** tissues. This will search all the tissues in
the list excluding the highlighted item(s).
- Select a single tissue and keep the "Include" button checked.
- Select two or more tissues and keep the "Include" button checked.
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ii) Tissue Preparation |
The default setting is all library preparation
methods (described
in Tissue Preparation Overview) or choose one specific method or
several.
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iii) Tissue Histology |
The default setting is normal, pre-cancer, and cancer histology, or
choose one specific histology or several. |
iv) Library Protocol |
The default setting is all library protocol methods, or
choose one specific protocol or several. The protocols
listed below the line are CGAP specific protocols described in
cDNA Library Protocols Overview.
|
v) Library Name |
Enter a full or partial library name, e.g. NCI_CGAP_Pr1,
NIH_MGC_50, or Pr.
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**
To choose multiple items in a select box, hold down the following keys together
as you click on each item:
- In a PC: [CTRL] and [Alt]
- In a MAC: [Alt] and [Apple]
The range of possible queries is the same of for the cDNA xProfiler,
with the additional inclusion of the SAGE libraries. Below, the xProfiler examples
are repeated with additional queries.
Pool A | Pool B |
Human, normal breast | Human breast cancer |
Human brain cancer | Any human tissue, excluding brain
| Human cell lines of prostate cancer | Human bulk prostate cancer |
Normal human colon, normalized | Normal human colon, non-normalized |
Mouse CGAP library NCI_CGAP_Mam6 | Mouse CGAP mammary libraries |
Reviewing Selected Libraries in Pools A and B |
Having selected the criteria for Pools A and B and pressed Submit Query,
the "Review of Library Pools for DGED" page appears, which contains:
- The option to specify the expression factor (F).
The expression factor, in conjunction with the significance
filter (P), determines which results are reported. A result is
reported if the odds ratio is significantly greater than F
or significantly less than 1/F.
F is set by default to "2"
but this number may be set to any number greater than or equal
to 1. As F increases, fewer results will be reported.
- The option to specify the significance filter (P).
The significance filter, in conjunction with the expression
factor (F), determines which results are reported. A result is
reported if its significance is less than P. P is set by default
to ".01" but this number may be set to any number from 0 to 1.
As P increases, more results will be reported.
- Libraries chosen for each pool listed in a table.
- The first column is the Target Pool (A) and the second column is "Background (B).
The checked boxes indicate which library belongs to which pool.
- The next column provides the number of sequences in
the library.
- The last column lists keywords which describe the library.
It may be necessary to resort the libraries, e.g.,
to have all of Target followed by all Background libraries. To do this, click the back button
on your browser and choose the appropriate criteria in #4. Press submit again.
Carefully review the libraries before proceeding. Check there are no libraries of "pooled"
tissues or whole fetal tissue which may invalidate the results. Check that a library
is not in both groups. Remove certain libraries to narrow your original selection. When you are satisfied,
press Submit Query.
Understanding the DGED Results Page |
The results page contains:
- The UniGene Build number
- The total number of sequences or tags in each pool
- The total number of libraries in each pool
- A table listing the genes or tags found to be expressed with a
statistically significant difference
between pools A and B.
The following information is provided:
Field | Description |
Symbol | The gene symbol for the gene cluster that contains
two or more found sequences from the target pool. |
Gene Info | A link to the Gene Info page, which contains links
to gene information in other NCBI and NCI databases. |
Accession Number | Representative GenBank accession
number(s) for the gene |
Libs A (or B) | A link to the libraries which contain this gene |
Seqs A (or B) | The number of sequences found for a gene in either Pool A or B. |
Seq Odds (A:B) | The sequence to odds ratio uses a simple
mathematical formula to provide a measure of the relative amount of a gene in
pool A to Pool B. |
P value
|
A test of probability: the smaller the number, the more
likely the result is not due merely to sampling error |
Used together, the seqs odds ratio and the significance
test provide a measure of
confidence that the difference in the expression of a gene or tag is "real"
and not due sampling error.
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