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List only potential regulatory links that meet the selected filter criteria below.

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 menu below. Sorting is applied after filtering where possible (the exception being the "Top" filter) so the filters applied will affect the sort.

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# CisMapper

### Prediction of Regulatory Links

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

If you use CisMapper in your research, please cite the following paper:
Timothy O'Connor, Mikael Bodén, Timothy L. Bailey, "CisMapper: Predicting regulatory interactions from transcription factor ChIP-seq data", Nucleic Acids Research, 45:e19, 2017. [Abstract and Full Text]

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## Results

#### Potential Regulatory Links (score ≤ )

Gene ID | Gene Name | TSS ID | TSS Locus | Strand | RE Locus | Distance | Histone | Correlation | Corr. Sign | Score | RE Score | Best RE? | TSS Score | Best TSS? | Gene Score | RE Loci per TSS | TSSes per Gene
--- | --- | --- | --- | --- | --- | --- | --- | --- | --- | --- | --- | --- | --- | --- | --- | --- | ---

#### Filter & Sort

##### Filters

Top
Show only best TSS for each gene
Show only best RE locus for each TSS
Gene ID matches
Gene Name matches
TSS ID matches
TSS Locus matches
RE Locus matches
≤|Distance|≤
≤ Distance ≤
Correlation Sign
Score ≤
Gene Score ≤

##### Sort

#### Columns to display

Show Gene ID
Show Gene Name
Show TSS ID
Show TSS Locus
Show Strand
Show RE Locus
Show Distance
Show Histone
Show Correlation
Show Correlation Sign
Show Score
Show RE Score
Show best RE
Show TSS Score
Show best TSS
Show Gene Score
Show RE Loci per TSS
Show TSSes per Gene

## Input Files

#### Locus File

File Name

#### Annotation File

File Name | File Type | Number of TSSes with Links | Number of Genes with Links
--- | --- | --- | ---

#### Other Settings

RNA Source |
Tissues |
Histone Root |
Histone Names |
Maximum Link Distances |
Expression Root |
Expression File Type |
Transcript Types |
Minimum Feature Count |
Minimum Maximum Expression |
Maximum HTML Score |

##### CisMapper version

(Release date: )

##### Command line summary