Genome Explorer Central GeneIndex database component; Portal for accessing genomic entities, annotations, relations and search results; Tools and viewers for in-depth analysis of locus-associated functional features and for ortholog and protein family prediction; Visual genome-genome comparisons including syntheni analysis and model organism evaluations; Interactive viewers to align and analyze splicing variants on RNA and protein level, EST alignments, functional annotation tools.

Promoter Explorer Database to store and structure gene regulatory wiring schemes; Tools to predict and annotate promoter structures and related transcription factor binding sites; Tools to identify other regulatory elements such as miRNA target sites; Portal for direct access to transcription factors, position weight matrices or TFBS;Interactive tools for in-depth analysis of predicted and experimentally derived promoter structures; Integrated analysis of gene expression data and promoter architectures

Signaling Explorer Comprehensive database to store signaling pathway data and regulatory network structures coming from different sources; Tools for automatic reconstruction of signaling pathways, for network analysis and expression data integration; Portal for direct access to pathway maps, interacting proteins, metabolites, nucleotides, co-factor and related reaction evidences; Viewers and tools for in-depth analysis of mRNA and protein profiling data mapped to signaling pathways; Interactive drawing and sharing of custom signaling maps.

Pathway Explorer Database for storage of metabolic pathways, including metabolites, enzymes, protein complexes, co-factors, reactions, stoichiometry and pathway maps; Portal for direct access to pathway maps, chemical compounds, biochemical reactions and enzymes; Enzyme categories incl. EC numbers; Interactive tools to edit and visualize metabolic pathways, to compare metabolic capacities across different organisms, and to map Tx, Px and Mx onto metabolic pathways.

Sequence Explorer Portal for integrated analysis and result management of all proprietary and public sequences and analysis tools such as BLAST searches, motif identification and sequence alignment; Plug-in interfaces to register and integrate proprietary analysis tools; Tools for comparative study of amino acid and nucleotide sequences, multiple sequence alignment, phylogenetic trees and protein and DNA feature displays; Direct integration with a variety of modules and resources coming with Phylosopher`s Sequence Data Center.

Expression Explorer Tools for mapping probe sequences to genome sequences and mRNA databases; Interfaces for handling standard microarray technologies (incl. Affymetrix, Agilent etc.) and RT-PCR data (incl. TaqMan primers); Portal for direct access to probes, primes and other reagents to genes, transcripts and proteins; Integrated locus view of probe and primer mapping; Gene-centric viewer of molecular profiling data across multiple samples ("electronic northern"); Data structures to store and categorize biomaterial used in expression studies.

Literature Explorer Database for storing literature information in a PubMed compatible format; Literature data directly referenced to molecular entities in GeneIndex; Portal for direct access to articles and integration with genes, proteins, transcripts, experiments and transcription factors; Tools like PubMedAgent for automated import and updates of references.

Sequence Data Center Relational database framework for storing and managing large sequence and annotation databases; integrated freely configurable agent framework for automatical updates of public sequence databases; high performance, alert mechanisms; tightly integrated with Sequence Explorer module, providing tools to screen for sequence patterns, and interfaces to trigger index (e.g. Blast indices) generation.

Xtend API Integrates target-relevant information stored in external systems, including screening and pharmacology databases, patent information and management applications; supports and integrates configurable dynamic queries and features integration with gene compendia, integrated queries and real-time information synchronization; standard adapters available for Expressionist (cross-omics) data integration.

More than 2000 pages of HTML Documentation include FAQs and HowTo's as well as pages for the Explorers, system administration, agent documentation and Perl API.

The Phylosopher core features a comprehensive Oracle database, a portal for accessing and navigating the database, and APIs for seamless in-house integration.

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