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.


Asuragen has partnered with Ingenuity Systems, Inc., to link expression profiling data to molecular pathways and processes. Ingenuity Pathways Analysis (IPA) is the industry standard for rapid and precise identification of biological mechanisms, pathways, and functions most relevant to experimental datasets or genes of interest.


Using a different approach, 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.


IPA and GSEA methodologies are based on databases that independently or together provide a wealth of biological insight into molecular profiling data. In the Ingenuity Knowledge Base, all biological and chemical relationships are manually curated and modeled by a team of Ph.D. scientists, and are supported by experimental evidence published in the peer-reviewed literature. 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

    • Ingenuity Pathways Analysis (IPA)
      • Interactive results linked to literature sources

      • We provide a limited-term, full-access license to you for viewing and exploring results directly in IPA from your own desktop

      • Receive full technical support directly from Ingenuity Systems experts as you review your results

    • 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 IPA Service:
    • Creation of a priori definitions of transcripts that are members of particular biological pathways or processes using IPA software and open source databases

    • Formatting, uploading, and processing of expression profiling data to generate lists of significantly changed genes using statistical methods appropriate for your study

    • Export of these lists into IPA to generate networks of genes based on a 6-step process

    • Comparison of lists of significantly changed genes with each biological process or pathway of interest in the IPA database

    • Explore your results directly in IPA from your own desktop using a limited-duration, full-access license provided by Asuragen

    • Receive full technical support directly from Ingenuity Systems experts as you review your results


  • 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 IPA: Your personalized login and password to the Ingenuity system with your data pre-loaded and ready for your follow-up analysis.


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:

CS0014  Data Analysis, Additional IPA Group Comparison
CS0015 Data Analysis, Data in IPA Compatible Format
CS0013  Data Analysis, IPA 30-Day License & Data Upload
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.