BiC Provides:

Expression microarray data analysis
Copy number variation genotyping data analysis
Nucleic acid and protein sequence data analysis
Integrated genomic/genetic analyses
Scripting and coding services
Training services

The BiC can conduct many types of analyses on data from a variety of measurement platforms and for various research-based and clinical protocols.

Several platforms are currently popular with our research community, and we strive to support expert analysis using these platforms as our primary service. However, other measurement platforms, especially those of leading-edge character, are always of interest to us.

If your particular research area or measurement platform is not listed in our main services, please contact us, as there are ways we deal with unique analyses:

• We can apply general, well-known bioinformatics principles and techniques to your research, regardless of specific expertise on that platform.
• We can utilize the researchers within our extensive parent organization, the Center for Biomedical Informatics (CBMi) <link1.1>, to facilitate a more extensive research activity.

Primary Service Offerings:

Expression Microarray Data Analysis: We work closely with the Nucleic Acid/Protein (NAP) Research Core to perform analyses and consultation, including:

• Study design
• Data quality assessments
• Normalization and summarization procedures
• Appropriate signal filtering
• Significance testing according to study design and goals
• Predictive modeling and classification
• Pathway and ontology enrichment analysis
• Researcher-specified analyses

We deliver results after interacting with researchers to ensure a complete understanding of the research and where the microarray data "fits in." In addition, we interact with researchers as their analysis progresses to assess how results correlate with expectations and to modify the analysis plan accordingly. Therefore, we request a certain degree of face time from researchers to maximize the analysis outcomes, deliverables and interpretation.

Contact us for access to any service or to ask questions.

Copy Number Variation Data Analysis: We take full advantage of our close collaborations with the NAP Core and with the Center for Applied Genomics (CAG) in order to offer estimates of copy number variations from genotyping microarray data. The services include:

• Study design
• Data quality assessments
• Identification of copy number regions
• Linkage of variants to disease phenotypes
• Commonality of variant regions across individuals
• Functional analysis of variant regions

This fairly new type of analysis has revolutionized our internal research and development services. We expect that the demand for this type of analysis will be high in the Children's Hospital research community. We are currently developing a set of easily accessible tools that will be able to perform a comprehensive copy number variation analysis. Stay tuned for updates on the development of these tools.

Contact us for access to any service or to ask questions.

Nucleic Acid and Protein Sequence Analysis: The BiC analyzes any size sequence dataset, from simple single-gene analyses to multi-organism comparisons. Our sequence analysis services include:

• Gene and protein homology and similarity assessments
• Comparative genomics analyses across multiple species
• Gene prediction
• Sequence-based functional classification

Contact us for access to any service or to ask questions.

Integrated Genomic/Genetic Analyses: The future growth of bioinformatics lies in developing capabilities for identification of biologically relevant gene behavior or gene networks as measured by a number of platforms. The integration of expression microarrays, whole genome association arrays, fully annotated sequences, and other functional genomics data allow for more powerful assessments. Current services provided by the BiC include:

• Visualization and analysis of genomic sequences relative to genes, introns, exons, SNP and epigenomic entities
• Comparison of expression and copy number variation data
• Combinations of a variety of data types using well-tested bioinformatics methods

Contact us for access to any service or to ask questions.

Scripting and Coding Services: We can perform scripting tasks specific to your needs. Data processing scripts are our specialty and include the following types of activities:

• Data extraction from data-heavy files
• Data re-formatting into more user-friendly formats (e.g., tab-delimited, Excel, etc.)
• Scripting for batch processing of files or data

The script development service we offer is customized to your data and goals, has a quick turnaround, and does not involve a full-blown software development process.

Contact us for access to any service or to ask questions.

Training Services: We conduct training on various bioinformatics data analysis software packages for Stokes researchers, including:

• Gene expression microarray and functional genomics analysis using GeneSpring GX, Spotfire DecisionSite, Ingenuity Pathways Analysis and a variety of open source applications
• Nucleic acid and protein sequence analysis using Sequencher, MacVector, Discovery Studio Gene, VectorNTI Advance, Lasergene and phred/phrap/consed
• Publicly available biological database resources such as the University of California Santa Cruz's genome browser and sites hosted by the National Center for Biotechnology Information
• Tools developed by the Bioinformatics Core, such as MyBic

Contact us for access to any service or to ask questions.