T-Gene - Submission form

The chromosome locations (loci) of potential regulatory elements in BED format. Typically, these would be transcription factor (TF) peaks from a TF ChIP-seq experiment, output by a peak-caller such as MACS.

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Select genome release corresponding to your genomic locations (loci) along with a tissue panel of histone modification and gene expression data, if one is available for your genome release. T-Gene will score each potential regulatory link between a locus and a TSS, that are within 500,000bp of each other. (It will always score the closest-TSS and closest-locus links, regardless of distance.) If you choose a genome with a tissue panel, T-Gene will score each link by by combining the correlation between the histone modification at the locus and the gene expression of the TSS, across the panel of tissues, with the distance between the locus and TSS. If no tissue panel is available (or chosen), T-Gene will score each link based solely on the distance between the locus and the TSS. See the T-Gene Genomes and Tissue Panels documentation for more information on the available genomes and histone/expression panels.

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Set this to a value less than 1 to limit the size of the HTML and TSV output files. Set it to 1 if you want the HTML and TSV files to contain all possible links, regardless of their statistical significance.

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Enable this option if you want T-Gene to include a link to the closest locus for each transcript even if the link does not satisfy the maximum link distance requirement.

Enabling this option will make the T-Gene output substantially larger.

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Enable this option if you want T-Gene to include a link to the closest TSS for each locus even if the link does not satisfy the maximum link distance requirement.

Enabling this option will make the T-Gene output substantially larger.

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T-Gene - Prediction of Target Genes
../doc/images/tgene_icon.png: T-Gene Logo

Data Submission Form

Predict regulatory links between genomic loci and genes.

loci Input genomic locations Upload a BED file of genomic locations (loci) to analyze. FILE register_component tgene_panel Select the genome and tissue panel Choose the genome and histone/expression panel (if available).

### Set the maximum p-value for links in T-Gene's output files

Link p-value ≤

### Include closest locus links

Include closest locus links

### Include closest TSS links

Include closest TSS links