Download contents of the "Potential Regulatory Links" table as a tab-separated values (TSV) file suitable for use with programs such as Excel or for uploading to programs for gene enrichment analysis (e.g., GOrilla) First choose the columns of information you wish to download, then choose how you want the links to be filtered and sorted, using the check boxes and sorting menu on the right. Then click on this button and the links will be downloaded in a file named "tgene_links.tsv" on your computer.
List only potential regulatory links that meet the selected filter criteria below. Select the desired filters below, then click the Update Filter & Sort button located below.
The first two filters ("Links/Genes/TSSes/RE Loci" and "Top" are applied after sorting the links. All other filters are applied before sorting.
The first filter affects the overall content of the report as follows:
|Links||Show all links (subject to the other Filters and the Sort).|
|Genes||Show the top TSS for each Gene (subject to the other Filters and the Sort).|
|TSSes||Show the top RE Locus for each TSS (subject to the other Filters and the Sort).|
|RE Loci||Show the top TSS for each RE Locus (subject to the other Filters and the Sort).|
The second filter ("Top") limits the output to at most 2000 top links.
Sort the potential regulatory links according to the criterion selected in the drop-down menu below.
Sorting is applied after filtering except for the first two filters.
If a tissue panel was provided, ties in the sorting field are resolved by sorting on the following fields, in order: CnD_P_Value, Correlation_P_Value, TSS_ID, RE_Locus, Histone.
If no tissue panel was provided, ties in the sorting field are resolved by sorting on the following fields, in order: Distance_P_Value, TSS_ID, RE_Locus, Histone.
For further information on how to interpret these results please access https://meme-suite.org/meme/doc/tgene-output-format.html. To get a copy of the MEME software please access https://meme-suite.org.
If you use T-Gene in your research, please cite the following paper:
Timothy O'Connor, Charles E. Grant, Mikael Bodén, Timothy L. Bailey, "T-Gene: Improved target gene prediction", Bioinformatics, 36(12):3902-3904, 2020. [Full Text]
|Potential Regulatory Links||Program information||Links in TSV Format|
|Maximum Link Distances|
|Use Gene IDs|
|Low Expression Correlation Adjustment Threshold|
|Include CL (Closest Locus)|
|Include CT (Closest TSS)|
|Add noise to zero expression and histone values|
|Random number seed|
|Number of Permutations|