Table 1 Bioinformatics Resource Manager (BRM) v2.3 capabilities

Data Management

XREF Identifier Retrieval

• Organization and Storage

• Gene Identifiers (NCBI)

• Versioning

• Protein Identifiers (UniParc)

• Meta-data tracking

• Cross Species Orthologs (Ensembl)

• Importing data from clipboard, EDMS

• Prokaryotic Identifiers (CMR)

Data Processing and Editing

miRNA Datasource Retrieval

• Dataset Merging

• miRNA Predicted Targets

• Table Features (OpenOffice Calc)

• (TargetScan, microCosm, microRNA)

• Extraction of Embedded Data/IDs

• miRNA Identifiers

• Column Merging/Splitting

• miRNA Metadata

• Duplicate Row Removal

• Edit Column Headers

DatWorkflows

• Affymetrix QC/Normalization (R)

Batch Annotations Retrieval

• Network Inference (CLR, Pearson)

• Gene Ontology (GO)

• Pathways (KEGG)

Data Analysis and Visualization*

• Gene Annotation (NCBI, CMR, miRNA)

• Clustering (MeV)

• Protein Annotation (Uniparc, CMR)

• Network Visualization (Cytoscape)

• Protein Interactions (BIND, Prolinks)

• Functional Enrichment (DAVID)