Convert site models to proteins (analysis)

Analysis "Matrices to molecules" is designed to convert site model IDs (e.g. matrices) into transcription factors.

As input, any table with site model IDs (e.g. matrices) can be taken. Such tables may result from several analyses including "Site search on gene set" and "Site search on track".

For this conversion, the links between transcription factors and matrices, as they are curated in the corresponding database, are used. The database is selected based on the profile you choose. Currently you can choose either TRANSFAC or GTRD profiles. Output from "Matrices to molecules" is a list of transcription factors as a gene set. Type of identifiers for the resulting table can be selected in the field "Output type". Table of transcription factors resulting from this analysis can be used as input for other analyses, for example, as input for master regulator search.

Parameters:

• Sites table – Select table with the results of "Site search on gene set". Such table contains site model ID in each row.
• Profile – Select the profile that was used for site search. In most of the cases, profile is selected automatically.
• Species – Select human, mouse or rat species
• Output type – Select type of identifiers for the resulting table
• Numerical value treatment rule – Select one of the rules to treat values in the numerical columns of the table when several rows are merged into a single one.

  In cases of "average", "average w/o 20% outliers" and "sum", the selected rule is applied to all numerical columns of the table. In cases of "minimum", "maximum" and "extreme" a new option appears bellow which request user to select a "Leading column". The chosen rule is applied then to the values in the selected Leading column (e.g. in the Leading column the maximum value is computed among all the merged rows). All other numerical values of the table will be taken from that row which corresponds to the selected value in the leading column.

• Leading column – Select the column with numerical values to apply one of the rules described above
• Output table – Path to store the resulting table in the tree