About TBFuncGeno Database:
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TBFuncGeno: TB gene expression database developed at Pacific TB and Cancer Research Org

This database is linked to other TB-related or resource databases:
(1) WebTB: TB research resources provided by the TB Structural Genomics Consortium.
(2) TBDB: An integrated platform for TB research.
(3) TubercuList: M. tb. genome annotation.
(4) MTB Gene List: Functional classification of M. tb. genes.
(5) GEO: A comprehensive gene expression database (omnibus) provided by NCBI at NIH.
(6) CDC: Centers for Disease Control and Prevention: TB Elimination.
(7) PubMed: Access to biomedical research publications.
(8) KEGG: Kyoto Encyclopedia of Genes and Genomes.
(9) TB Persistence Targets: Top 100 M. tb. persistence-related gene targets.
(10) MTBReg: Analysis of gene expression and regulation data in M. tb.
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Instructions for using the TBFuncGeno Database:
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Please note that this database is at the initial stage of development.
The current content may be limited.

This database allows you to query about any gene or open reading
frame in Mycobacterium tuberculosis H37Rv genome.
When you submit a gene name or a Rv name, the system will return
the associated microarray data values and information
in the database. 

[Keyword-Based Search:]
Keywords are used to index each microarray data set generated under 
conditions, such as hypoxia, acid, isoniazid, rifampin, drug, ...
Keywords sometimes are extracted from the title of the source 
publications. Keyword-based search helps narrow down the search of
the microarray data records of interest. 

In search of the records, the user must enter a gene name or a Rv name.
The user may also enter keywords (a single or multiple words separated by 
a space between two words).
If keywords are entered, only those records whose associated keywords
contain the entered keywords will be displayed.
If no keyword is entered, then those records associated with the entered
gene name or Rv name will be displayed.

<Keywords examples:>
 isoniazid, INH, capreomycin, resistance, clinical-isolate, in-vitro,
 drug, log-phase, exponential-phase, etc. 

If the result table is too large to fit your computer screen, please
use the scroll bar to move the screen rightward and/or downward.
Note that you should be able to see the eleven attributes for each result:

1. Gene name: e.g., dnaA, dnaN, recF, gyrB, gyrA, etc
2. Rv name: e.g., Rv0001, Rv0002, Rv0003, Rv0004, Rv0005, etc.
3. Signal: The strength of the signal detected from microarray
       hybridization, reflecting the level of gene expression
       at a given condition.
4. Detection: Indication of whether a measured 
          transcript is detected (P Call), not detected (A Call),
          or marginal/borderline (M call).
5. Detection p-value: The statistical p-value associated with the Detection Call.
6. Signal log ratio: The logarithm (base 2) of the ratio of the signal at
          the test condition to the signal at the control condition.
          A signal ratio of 1 means a two-fold increase.
          A signal ratio of -1 means a two-fold decrease.
7. Change: Indication of whether there is an increase (I), 
           decrease (D) or no change (NC) in gene expression 
           when comparing the test condition to the control condition.
8. Change p-value: The statistical p-value associated with the Change Call.
         We suggest that statistical significance is defined by
           P < 0.000001 for the I (Increase) call and (1 - P) < 0.000001
           for the D (Decrease) call.
9. Gene information: A hyperlink to the web page containing the 
            information about the gene under query stored at the gene 
            database of the NCBI web site. Navigate to that page by
            clicking on the hyperlink.
10. Source: A hyperlink to the publication stored at the PubMed database.
           The publication describes the details about the microarray
           experiments.
11. MIAME: A hyperlink, upon clicking, shows the information about the 
           microarray experiments. according to the MIAME 
           (Minimum Information about Microarray Experiments)
           standard for reporting microarray data, including a description 
           of experimental design, array design, samples, hybridization, 
           measurements and normalization controls. 

[Note 1:] If there is no control condition, the attributes 6-8 will
          be blank.
[Note 2:] The attributes 3-8 are based on the Affymetrix oligonucleotide
          GeneChip format. For cDNA microarrays, the attributes
          3-5 and 7-8 will be left blank.

[Generate Excel:]
The table of the retrieved records can be downloaded by 
clicking on the box labeled "Generate Excel" above the data table.
The user can conduct analysis on the data using the built-in
Excel functions.