Index

1. Summary
2. Input
3. Options
4. Output

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1. Summary

This query allows the user to search for the Transcription Factors (TFs), included in the YEASTRACT database, involved in the regulation of a given list of genes.

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2. Input

The input required is a list of S. cerevisiae genes or ORF names.

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3. Options

The user may select to search for TFs that have been experimentally shown to regulate the expression of the genes (i.e., documented associations) or for TFs whose consensus binding site matches a subsequence of the promoter region of the genes (i.e., potential associations).The combined result of the two aforementioned search modes can be obtained using the search option 'Both'.
Furthermore, the user may restrict its search to the regulatory associations identified based on direct or indirect evidences. Direct Evidence was considered to be provided through experiments such as Chromatine ImmunoPrecipitation (ChIP), ChIP-on-chip and Electrophoretic Mobility Shift Assay (EMSA), that prove the direct binding of the TF to the target gene's promoter region, or such as the analysis of the effect on target-gene expression of the site-directed mutation of the TF binding site in its promoter region, which strongly suggests that the TF interacts with that specific target promoter. The classification Indirect Evidence was attributed to experiments such as the comparative analysis of gene expression changes occurring in response to the deletion, mutation or over-expression of a given TF. The complete enumeration of the experimental approaches considered to provide direct or indirect evidences is provided in Table Evidence code list.

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4. Output

When the search is performed for documented associations, the output is a table containing, for each gene, the list of transcription factors that regulate that gene, links to their entries in the YEASTRACT database and links to the publications where the relationship between the gene and the TF was identified.

A search for potential associations between genes and TFs returns a similar output as the search for documented associations, including in addition the TF binding site that was matched in the promoter of the gene. There is an additional option in this case, of the generation of an image (by selecting the box labeled Image). This image depicts the promoter region of each gene and displays the subsequences of the gene that match the binding site consensi of the transcription factors in the database. An example is shown below, for the gene AAC2. Each vertically coloured bar represents one potential TF binding site.

By default, the previous figure is generated to show all the TF binding sites of all the TFs found to have at least one potential binding site in the given promoter region. The figure can be altered by selecting or deselecting the TFs for which the potential binding sites are to be displayed, using the checkboxes shown in the figure below:

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