Pathway Analysis


As an independent service offering or paired with Asuragen’s molecular profiling services, our Pathway Analysis services can save you days or weeks in identifying biologically interesting patterns in your data. For expression profiling of clinical samples, we can help you identify potential mechanisms of action for existing therapies and discover potential novel therapeutic targets.


Gene Set Enrichment Analysis1 (GSEA) is a computational method used to assess whether an a priori defined set of genes (characterizing a biological process, located in the same chromosomal area, sharing the same GO2 category, or sharing common regulatory motifs) shows statistically significant differences between two conditions.


GSEA methodology is based on databases that independently or together provide a wealth of biological insight into molecular profiling data. The GSEA team maintains the Molecular Signature Database (MSigDB), composed of gene sets from several publicly available, manually curated databases in addition to gene sets linked by positional, motif, or computed information. Learn more about Asuragen’s molecular profiling capabilities.


Description of Services
Deliverables
Additional Services Available
Catalog Numbers for Informatic Services
Requirements for Pathway Analysis and Related Services

Description of Services

  • Features of Pathway Analysis Services:
    • Data processing and pathway analysis is available in conjunction with Asuragen’s molecular profiling services OR as an independent service for your existing microarray data
    • Gene Set Enrichment Analysis (GSEA)1
      • Permutation-based methodology used to determine statistically significant pathways or processes (gene sets) represented in your data

      • Static results provided in a detailed web-format report DVD

  • Workflow for GSEA Service
    • Formatting, uploading, and processing of expression data exported into GSEA software

    • Ordering of your genes into a ranked list based on an enrichment score calculated in GSEA

    • Comparison with database to determine whether members of defined gene sets (e.g., reflecting pathways or common cytogenetic locales) cluster near the top or bottom of your ranked list, indicating a correlation with the phenotypic class distinction

    • Generation of a detailed report containing gene sets most significantly represented by your data

Deliverables

For GSEA: A DVD containing the extensive web-based data analysis from the GSEA implementation. Data may also be delivered by FTP or e-mail.


Additional Services Available

Sample prep:

Cell lines – eukaryotic and prokaryotic
Blood/biofluids
Frozen/RNAlater/RNAretain tissues
Fixed (FFPE) tissues

mRNA Analysis:
Affymetrix Gene Expression Profiling Services
Illumina Gene Expression Profiling Services
Applied Biosystems TaqMan Gene Expression Services

miRNA Analysis:
Ambion/Affymetrix DiscovArray miRNA Expression Profiling
Agilent Human miRNA Microarray Service
Applied Biosystems TaqMan miRNA Expression Services

DNA Analysis:
Applied Biosystems TaqMan Gene Expression or SNP Detection Services

Data Analysis:
Standard Service Premium
Full Service

Catalog Numbers for Informatics and Related Services

Pathway Analysis:

CS0010 Data Analysis, per Custom SOW (applies to GSEA)

Requirements for Pathway Analysis and Related Services

Sample Input Requirements for the services listed above are found in the Sample Submission Form and Shipping Instructions


1Subramanian, A., P. Tamayo, V. K. Mootha, et al. (2005). "From the Cover: Gene set enrichment analysis: A knowledge-based approach for interpreting genome-wide expression profiles." Proceedings of the National Academy of Sciences 102(43): 15545-15550.


2Ashburner, M, et al. (2000). Gene ontology: tool for the unification of biology. The Gene Ontology Consortium. Nature Genetics 25(1): 25-29.