PlasmoTFBM is a comprehensive relational database to store putative regulating elements and their related information, 
including the gene expression data, significant motifs generated by AlignACE and MotifRegressor, modules generated by 
ISA (Iterative Signature Algorithm), and gene annotation information including the functional information and the 
chromosomal location.

This document gives an example to query the PlasmoTFBM.

1. To get start, click the “Querying PlasmoTFBM” on http://biorg.cs.fiu.edu/TFBM/.

2. Enter a set of genes separated by space on opened webpage. In this example, suppose we are interested in gene set 
   “MAL13P1.60 MAL7P1.86”.

3. Click “Get Modules” to get all the modules containing gene MAL13P1.60 MAL7P1.86.

4. Choose any module then click “Explore Module” to get the genes contained in selected module and associated conditions 
   (time points). Suppose module “MAL7P1.86_g2_c6” is chosen, after “Explore Module”, we can see bunch of  genes containing
   in module “MAL7P1.86_g2_c6” and time point “43 42 44 27 41 1 45” which is the conditions associated with this module.

5. To get motifs of particular gene, select any gene interested (one gene only), along with time points associated 
   (use Ctrl+ Left mouse click to choose more than one time points) and extract option (either MotifRegressor or AlignACE 
   or BOTH), then click “Get Motif”. Suppose we want to explore the motifs from both MotifRegressor and AlignACE in gene 
   MAL13P1.60 at all conditions, then all the time points, gene “MAL13P1.60” and extract option “BOTH” are selected in this
   example.

6. After step 5, either “Explore Motif” or “Explore Gene” can be conducted. 

   If we want to explore motif, select one or more (use Ctrl+ Left mouse click to choose more than one motifs) motifs in 
   “All Motifs” column, then click “Explore Motif” to get genes having selected motif respectively.

   To explore gene, first select interested genes in “Genes” column (use Ctrl+ Left mouse click to choose more than one
   genes),  then select interested motifs in “All Motifs” column (use Ctrl+ Left mouse click to choose more than one motifs),
   click “Explore Gene” to open query result on new page. 

   Note: In the opened result webpage, motifs labeled + are on the forward strand, while the ones labeled – are on the
   reverse strand.  

7. Click “Reset” button to begin a new querying.

User can query PlasmoTFBM for any interested gene set. Gene set on http://biorg.cs.fiu.edu/TFBM/ is another example. User can
use it to explore G-box motifs in the gene set.