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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:

Value | Resulting Report
--- | ---
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.

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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# T-Gene

### Prediction of Target Genes

For further information on how to interpret these results please access http://meme-suite.org/doc/tgene-output-format.html. To get a copy of the MEME software please access http://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

#### Potential Regulatory Links ( p-value ≤ )

Gene ID | Gene Name | TSS ID | TSS Locus | Strand | Maximum Expression | RE Locus | Maximum Histone Level | Distance | CL | CT | Histone | Correlation | Corr. Sign | Corr. p-value (unadjusted) | Distance p-value (unadjusted) | CnD p-value (unadjusted) | q-value
--- | --- | --- | --- | --- | --- | --- | --- | --- | --- | --- | --- | --- | --- | --- | --- | --- | ---

#### Filter & Sort

##### Sort

##### Filters

Links Genes TSSes RE Loci
Top
Gene ID matches
Gene Name matches
TSS ID matches
TSS Locus matches
RE Locus matches
Maximum Expression ≥
Maximum Histone Level ≥
≤|Distance|≤
≤ Distance ≤
CL (Closest Locus) matches
CT (Closest TSS) matches
Histone matches
Correlation Sign
Correlation p-value ≤
Distance p-value ≤
CnD p-value ≤
q-value ≤

#### Columns to display

Show Gene ID
Show Gene Name
Show TSS ID
Show TSS Locus
Show Strand
Show Maximum Expression
Show Maximum Histone Level
Show RE Locus
Show Distance
Show CL (Closest Locus)
Show CT (Closest TSS)
Show Histone
Show Correlation
Show Correlation Sign
Show Correlation p-value
Show Distance p-value
Show CnD p-value
Show q-value

## 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