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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.

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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:

ValueResulting Report
LinksShow all links (subject to the other Filters and the Sort).
GenesShow the top TSS for each Gene (subject to the other Filters and the Sort).
TSSesShow the top RE Locus for each TSS (subject to the other Filters and the Sort).
RE LociShow 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.

To filter on "Gene_ID", "Gene_Name", "TSS_ID", "TSS_Locus" or "RE_Locus", you can enter any Javascript regular expression pattern. See here for documentation on Javascript regular expression patterns.

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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.

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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]

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Results

Filter & Sort

Sort 
Filters 

Columns to display

Input Files

Locus File

Annotation File

Other Settings

Transcript Types
Maximum Link Distances
Maximum p-value
Tissues
Histone Root
Histone
RNA Source
Expression Root
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
Noise Fraction
T-Gene version
(Release date: )
Command line summary