OSU Department of Biomedical Informatics

Services: Main | Consulting | Software Research Institute | CCC Shared Resource

Biomedical Informatics Shared Resource Consulting Service

The Biomedical Informatics core of the OSU Comprehensive Cancer Center is a consulting service for the analysis, interpretation, and presentation of high throughput data, and this core provides a service in data management, archiving, and software development.

The most common use of this core is for analysis of microarray data (for gene expression or ChIP-chip) and the identification of affected genes. Further, pathway analysis allows the biologist to identify the affected system and to predict upstream effectors and downstream consequences. Many bioinformatics experiments can be done using publicly available databases and querying these resources in ways not originally envisioned by the depositors, saving the experimentalist from the need (and expense) of carrying out a redundant microarray.

Data pipelines are now being set up to permit seamless transfer of data from the microarray shared resource to the bioinformatics core and to the biologist who generated the data.

Image analysis is also available in this resource.

Please contact the biomedical informatics core at Informatics@bmi.osu.edu to arrange for consulting.

Our fee structure is available at the bottom.

Microarray Analysis

  1. Planning and experimental design
    • Meeting to discuss the biological question
    • Checking database for existing relevant data
    • Providing advice on experimental design including (but not limited to) choice of genechips, number of replicates, selection of control, etc.
  2. Microarray image analysis and quality control
    • This step is usually done by the Microarray Core. We can provide service if necessary.
  3. Data normalization and identification of differentially regulated genes
    • Most commonly used service. Provide the following documents (if applicable)
      • Normalized data with gene symbols (excel spreadsheet by default)
      • List of differentially regulated genes (based on selection criteria agreed by the researcher – if not specified, will use p-values from t-test and mean fold change) – output file is in html format or excel spreadsheet
      • Standard plots (MA plot, volcano plot, etc).
      • Submission to Gene Expression Omnibus (GEO) maintained by NCBI (to comply with the NIH data sharing requirements)
      • For common chips with reasonable amount of samples (not too much curation), 2-5 hours is reasonable.
      • For uncommon chip platforms, longer time may be necessary.
    • In development, miRNA chip, ChIP-chip, and ChIP-Sequencing analysis.
  4. Advanced analysis
    • Most of these analysis items are customized. Some analysis is best if the client works together with the core staff.
    • Gene ontology (BiNGO, IPA, GO)
    • Pathway analysis (IPA, Pathway Studio, GenMapp?)
    • Correlation analysis (correlation with single genes, multiple genes, multiple datasets, often combined with pathway analysis)
    • Comparison study on multiple datasets
    • Clustering
    • Classification
    • Dynamics (for time-course study)
    • Transfac
    • Other analyses
  5. Verification/validation/interpretation
    • We provide help on validation using existing datasets and design of new microarray experiments.

Notes:

  1. Microarray experiments are carried out by the Microarray shared resource at OSU led by Dr. Liu.
  2. Biostatistics shared resource also provides service on analyzing microarray data.
  3. For studies in which we have substantial involvement and collaborative studies, we require co-authorship in publications.

Image Analysis

This figure provides a subset of the tasks that we can do. Given the nature of this area, most tasks will be domain-specific and customized (except for some simple image processing tasks).

Notes:

  1. We do not provide imaging equipment services. For digitization of histological images, the users can contact the Dept. of Pathology or the Mouse Phenotyping Shared Resources at OSU for accessing the Aperio Scanscope scanners. For other microscope use, please contact the Campus Microscopy & Imaging Facility led by Dr. Richard Burry (BRT205).
  2. We do not provide art or illustration services. The image enhancement work is provided only if it is necessary for image analysis or it has to be done using algorithmic tools.
  3. For studies in which we have substantial involvement (such as development and implementation of new or complicated algorithms) and collaborative studies, we require co-authorship in publications.

Fees for Services

Inside OSUCCC Outside OSUCCC
Bioinformatics consulting $50/hour $120/hour

These rates are temporary introductory rates. All services are priced similarly according to the time required. Special collaborative rates are available.

Standard analysis of microarray results from common platforms from fewer than 10 chips would be predicted to require about 2 hours.