Introduction to BKL Tools for Gene Regulation Analysis

BKL Gene Regulation Analysis Tools comprise specialized tools for predicting transcription factor binding sites, analyzing promoters, creating and comparing positional weight matrices, and for identifying miRNA regulators. Brief descriptions of the BKL Gene Regulation Analysis Tools are provided below, with hyperlinks to detailed information. A view of the interface used to access BKL Gene Regulation Analysis Tools is shown in the figure below.

Gene Regulation Analysis Tool Menu

Step-by-step data analysis

Use this easy, step-by-step workflow for guided analysis of microarray, ChIP-seq and RNA-seq data.

Learn more about the Step-by step analysis.

Please note: The step-by-step workflow is only available by subscription to the TRANSFAC module. Some parts of the analysis, particularly the identification of shared networks, will require in addition a subscription to PROTEOME.

Predict transcription factor binding sites

Use the Match tools (Match, FMatch, CMsearch) to search for transcription factor binding sites in a DNA sequence, either using matrices, profiles and composite models from the TRANSFAC matrix library or using customized matrices, profiles and composite models generated with the accompanying Match Profiler, Matrix and Composite Model Creation tools, respectively.

Learn more about Match, Match Profiler, and Matrix Generator tools.

Please note: The TF-binding site prediction tools are only available by subscription to the TRANSFAC module.

Create and compare matrices

Use the suite of Matrix tools to create and upload positional weight matrices, to compare a matrix against the TRANSFAC matrix library, or to cluster a set of matrices based on their similarity. Saved matrices can be also be viewed, deleted, or downloaded via the manage matrices option.

Please note: The Matrix tools are only available by subscription to the TRANSFAC module.

Identify miRNA regulators

Use the miRNA analysis tool to analyze genes for the presence of shared miRNA binding sites.

Learn more about the miRNA analysis tool.

Please note: The miRNA analysis tool is only available by subscription to the TRANSFAC module.