Overview

ExPlain is a software platform that facilitates the analysis and biological interpretation of large-scale data sets, such as those generated by DNA microarray experiments, proteomics, ChIP-on-chip or Chip-Seq as well as other high-throughput experiments.

Flexible workflows systematically guide you through the process of identifying the transcription factors and key signal transduction molecules that are unique for your data set, ultimately leading to generate experimentally testable hypotheses regarding relevant transcription regulatory and signal transduction networks.

Here are a few of the exciting capabilities of ExPlain.

Single-click Workflow

Allows you to easily analyze your data in order to accomplish the following highlighted tasks.

• Perform comprehensive promoter analyses.
• Predict prospective drug targets.
• Reveal disease biomarkers.
• Explain mechanisms of drug toxicity.

Support of Next-Generation Sequencing Technology

• ExPlain supports the upload and analysis of various NGS data results, including ChIP-on-chip, tiling arrays, and ChIP-seq, among others. 

Promoter Analysis

• Identify significant transcription factor binding sites.  The leading standard transcription factor database previously known as TRANSFAC, now incorporated into the BIOBASE Knowledge Library (BKL), is used as the basis for searching new binding sites of known transcription factors.
• New motif search (Seeder) algorithm. This algorithm allows you to identify novel motifs within a set of DNA sequences. Once identified, you are able to generate position weight matrices (PWMs) from promoters containing the novel motifs for use in additional analyses.
• TRANSFAC Patch algorithm. This pattern-based search for transcription factor binding sites is an alternative method for identifying those binding sites for which a PWM has not yet been described. As such, it is especially useful for identification of binding sites of novel transcription factors for which only a few sites are known.
• Identify Composite Regulatory Modules. ExPlain offers you the Composite Module Analysis (CMA) algorithm, which will identify regulatory modules or specific combinations of several binding sites in the promoters of your gene set.

Functional Analysis

• Extraction of manually curated expression and GO assignments from the BIOBASE Knowledge Library (BKL) ensure that the most reliable functional assignments are made available for data analysis.
• Incorporation of new public ontologies, such as Swiss-Prot keywords, allows functional analyses to include additional protein functions that are not covered by GO.

Network Analysis

• ExPlain provides you with the largest and most exhaustive hand curated database of signal transduction molecules, as well as powerful algorithms to identify key signaling molecules (key nodes) upstream or downstream of your genes of interest.
• State-of-the-art network visualization tools. You can easily visualize and modify the signaling networks relevant to your data. You van add the expression values of your data as well as your own proprietary interactions to enrich the network results.

Data Processing and Statistical Analysis Algorithms

• Support of Affymetrix exon array CHP files.
• Support of BioPAX3 format for importing interactions from external pathway databases such as Reactome and IntAct.
• Support of .tar and .gzip compressed file formats for bulk upload of large data sets.
• A novel statistical algorithm, called Rank Prod, for robust detection of differentially expressed genes, making it especially useful for analysis of very noisy data sets.
• A novel algorithm for clustering gene expression data, called CRC, for revealing clusters of co-expressed genes in array series such as time series, drug series, patient cohorts, etc.

Supported Organisms

• ExPlain provides support for human, mouse and rat data in its vertebrate version, and Arabidopsis, rice and soybean in the ExPlain plant version.
• The whole genomes and corresponding annotations are preloaded in ExPlain, including full promoter databases, your uploaded genes or microarray probes are automatically matched to the ExPlain database, providing you immediately with live links to promoters, transcription factors, signal transduction molecules, external database links and literature references.

To learn more about this product…watch an introductory video, read ExPlain publications, learn about the ExPlain Affymetrix Genechip^® compatibility, sign up for a free trial, or contact a sales representative.    

Working on plant gene expression?  Learn more about our ExPlain Plant version.