Gene Group | Search | Promoter Analysis | Cross Species

Gene Group

In Gene Group Analysis,you can enter a group of genes seperate with ";" and there are some parameters you have to set.
First,you have to choose the promoter region you want to analyze.Second,choose how many TFBS co-occurence you want analyze.Third,you can set the the support and cofidence score threshod which indicate how often these TFBSs co-occur in these promoter of genes.

After "Submit",a table will show you how often each pair of genes co-occur,and you can also get a graphical view to know the TFBS in these genes.

Search

In "Search" page,you can search by gene or transcription factor for different purpose:
1. To detect the TFBSs and their corresponding transcription factors (TFs),please search by gene.
2. To get annotation and transcription factor binding motif ,please search by transcription factor.

You can enter the Gene ID or Gene locus to search,the keyword search allows you to retrive all the description containg the query keyword.

After "Submit",you can get the gene annotation,including the KEGG pathway.GO term,sequence and other information.

In the bottom of the table,a graph shows the location of the query gene and its neighboring genes,and this helps you to choose the promoter regions for TFBS analysis.

After click the "Access the TFBS and trancription regulatory network",the promoter sequence you specify will be retrived for TFBS scanning,and a table lists all the TFBS found in this promoter.

After click "Co-express Analysis",there is a table shows you all the transcription factors identified from the last step which co-express with the query gene.

Promoter Analysis

In the first step of "Promoter Analysis",users can input a promoter sequence and choose what transcription factor they want to analyze.

There is a table lists all the TFBSs in the promoter,and more information such as binding sequence and position will be shown when the chehkbox is selected.

Cross Species

There are two functions in "Cross Species Analysis",to search the TFBS in the conserved regions in Arabidopsis and rice homologous genes,please use the first function, to search the TFBS in the conserved regions between two sequences ,please use the second function.

"Cross Species Analysis" allows the user to search the TFBS in the conserved regions between the homologous genes in Arabidopsis and rice.In the first step , just input an Arabidopsis Gene ID.

The result will show the gene annotation of each gene, and a table lists all the TFBSs in the conserved regions.

Department of Life Science and Technology,
Insititute of Tropical Plant Sciences Nation Cheng Kung University, Tainan, Taiwan
Contact with: Wen-Chi Chang