About TF binding site search
The function of this page is to predict the transcription factor (TF) binding site. You need two kinds of information to use this function. One is the information of the regions you want to search (reference regions). The other is information on transcription factor (TF conditions) you wish to search.
According to the conditions specified by the user, the program first prepares information on the binding region of all transcription factors in the genome. Both the sought and binding regions of transcription factors information are stored in the server as BED files. By intersecting these two types of BED files, the program outputs the hit area information as search results.
How to search
Reference regions can be decided from pulldown or from a BED file specified by the user. When "Keep order" is checked, the order of the TFs will be considered. When "Allow overlap" is checked, overlapping in TF sites will be allowed. (See below for details.)
For "TF conditions", you can add either "arbitrary sequence" or "predicted binding position of known transcription factor" as a prediction target. You can specify the "arbitrary sequence" pattern in the top dialog box. If "predicted binding position of known transcription factor" is desired, you can specify it from the lower pulldown.
Additional sequence pattern can be added from [Add sequence pattern] button. Similarly, additional TF can be added from [Add TF] button. When you click the buttons, the image of the hit pattern will be reflected in the bottom image. Next, when you click the [or] button, you can add conditions as "or" to the now specified TF region. With the [and] button, you can add a new TF region to a position next from the TF region specified immediately before. You can erase the previous condition by pressing the [Back] button at the bottom of the image. Up to 10 conditions can be specified.
When you have decided the condition, click the [Execute search] button. And then the search program will be executed.
* "Arbitrary sequence" uses GGGenome to obtain the hit position on the genome.
* "Predicted binding position of known transcription factor" obtains the hit position on the genome by using the result of ChIP-atlas.
About the search result:
Search results are displayed as table and genome browser. You can download intermediate results and final result (hit area and TF information hit at that position) as BED files. By clicking [Hit regions (BED)], you can download the results of the final hit region. From [Hit factors (BED)], you can download the hit region information of the TF whose binding is expected in the hit region. The information of "reference regions" used for the search can be downloaded from [Target regions (BED)]. When a BED file is uploaded, it will be pre-processed by the program, e.g., the name will be made unique and the length will be kept at maximum 255 characters. When the BED file is downloaded again, it will be the pre-processed file. Further, you can also download the BED files from GGGenome or ChIP-atlas results used by the program. In the result table, up to 100 lines of files downloaded from [Hit regions (BED)] are displayed. When you click "Go" located in the Browser column, its position will be reflected in the genome browser at the bottom of the screen.