Introduction to BKL Search, Tools and Data Management
BKL Search and Tools comprise powerful software solutions that facilitate searching for information in the BKL as well as specialized tools for analyzing customized lists of genes or miRNAs using BKL annotation, predicting transcription factor binding sites, visualizing pathways and building networks and much more. The parallel my data Data Management system provides a user-specific repository for storing the results of searches and analyses performed by the tools, along with data sets whcih have been uploaded by the user. Brief descriptions of the BKL Search, Tools and Data Management are provided below, with hyperlinks to detailed information. A view of the interface used to access BKL Search, Tools and Data Management is shown in the figure below.
BKL Search, Tools and Data management (tool view is shown)
BKL Search
Search
Use the Search tool on the start page to perform simple searches of general biological topics addressed in the BKL including genes/proteins, miRNAs, diseases, pathways, drugs, transcription factors and matrices. The search tools also provides options for uploading lists of genes, proteins and miRNAs in bulk as well as options for browsing selected content directly.
Learn more about the Search tools.
Please note: The diseases, pathways, and drugs Search options are only available by subscription to the PROTEOME module. The transcription factors and matrices search options are only available by subscription to the TRANSFAC module.
Ontology search
Use the Ontology search tool to browse the contents of the BKL by topic, browsing for genes, diseases or drugs that share common characteristics. In this way you are able to answer complex biological questions such as which genes are associated with a prostate but not ovarian cancer, which genes encoding G-protein coupled receptors are the targets of FDA approved drugs, and which drugs target proteins which are part of both the leptin and insulin signaling pathways - without tedious and oftentimes impossible literature searches.
Learn more about Ontology search.
Custom search
Use the Custom search tool to perform more detailed SQL-like searches for all entities contained in the BKL from basic biological entities such as genes, diseases and pathways to entities specific to the study of gene regulation such as sites, promoters, matrices and more.
Learn more about the Custom search tools.
Please note: Some Custom search entities are only available with the PROTEOME module while some are only available with the TRANSFAC module. See the overview of the Custom search tool for information.
BKL Tools
BKL tools are organized based on their application to functional analysis, gene regulation analysis or variant analysis.
Predict transcription factor binding sites
Use the Match tool to search for transcription factor binding sites in a DNA sequence, either using matrices or profiles from the TRANSFAC matrix library or using customized matrices or profiles generated using the accompanying Match Profiler or Matrix Creation tools, respectively.
Learn more about the Match, Match Profiler and Matrix Generator tools.
Please note: The Match tool is 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.
Analyze promoters
Use the ExPlain analysis system to perform advanced in silico analysis of high-throughput expression and other data through promoter modeling in order to identify causes for changes in gene expression.
Please note: The ExPlain analysis system is only available by a separate subscription.
View pathways and build networks
Use the PathFinder visualization tool to view canonical signaling and metabolic pathways and to build custom protein-protein interaction and gene regulation networks based on the curated data made available in the BKL.
Learn more about the PathFinder.
Identify shared attributes
Use the Functional Analysis tool to analyze a list of genes or miRNAs for the presence of statistically over-represented, curated attributes. The output is a list of curated attributes spanning up to eight different topics including GO molecular function, GO biological process, associated diseases, canonical pathways and more.
Learn more about the Functional Analysis tool.
Please note: The Functional Analysis tool is only available by subscription to the PROTEOME module.
Identify shared networks
Use the Network Analysis tool to analyze a list of genes for the presence of network clusters. The output is a list of protein interaction networks based on BKL curated data. These networks can be visualized, further edited and exported for publication via the linked BKL Pathfinder tool.
Learn more about the Network Analysis tool.
Please note: The Network Analysis tool is only available by subscription to the PROTEOME module.
Predict protein attributes
Use the BioKnowledge Transfer tool to assign predictive functions to submitted protein sequences based on domain structure and sequence similarity to more that 200,000 proteins spanning more than 20 species.
Learn more about the BioKnowledge Transfer tool.
Please note: The BioKnowledge Transfer tool is only available by subscription to the PROTEOME module.
BKL Data Management
The my data management system provides a centrally organized system for storing search results, reports generated by select analysis tools and data which has been uploaded by the user.