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
gene expression and
miRNA profiling 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
miRNA Microarray Service
Applied
Biosystems TaqMan miRNA Expression Services
DNA Analysis:
Agilent aCGH
Affymetrix SNP 6.0 - coming soon
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.