• Core Objectives
Director: Katheleen Gardiner, PhD
Co-Director: Tamim Shaikh, PhD
The objective of the Bioinformatics & Statistics Core is to provide advice, training and assistance in experimental design, data analysis and statistics, especially for research involving ID gene and pathway analysis, proteomics, genomics, and clinical and animal studies. The Bioinformatics & Statistics Core is designed as an information resource to complement and enhance the experimental tools provided by the other research cores. Bioinformatics & Statistics strives to provide IDDRC investigators with access to expertise, state-of-the-art software and datasets used in genomics, gene expression and pathway analysis, and to statistical expertise and tools used in design and analysis of genomics, clinical and animal studies, as well as any other complex IDD-related experimentation.
Investigators: Please remember to acknowledge your Colorado IDDRC affiliation and your use of the cores in all your published papers. For an example see the For Investigators web page.
1. IDD-focused bioinformatics.
Contact: Katheleen Gardiner, PhD
ID Gene Function and Pathway Database Website
This service provides Center investigators with comprehensive information on genes, gene products, and signaling pathways relevant to IDD. The database searches and tools are designed to aid both basic and clinical researchers in discovery and integration of IDD gene knowledge and in hypothesis generation. The IDD Bioinformatics facility is being built on “The chromosome 21 gene function and pathway database” initially developed for studies on Down Syndrome.
VIDEO: Gene Function and Pathway database
2. Bioinformatics for Microarray applications and HTS.
Contact: Tamim Shakih, PhD, Tzu Lip Phang, PhD
This service provides IDDRC investigators with access to expert consultation on, and assistance with, the analysis and interpretation of data obtained from genomic applications.
T. Shaikh is an expert in detection and interpretation of CNVs using multiple array platforms and analysis software. Software tools and expertise currently available for microarray and HTS analysis.
T. Phang has expertise in all aspects of expression data analysis including data normalization and filtering, hierarchical clustering, principal component analysis (PCA), QT clustering, 3D Data visualization and pathway analysis of modified genes. He has access to a wide range of computational tools and resources.
Contact: Misoo Ellison, PhD
This subcore offers expert advice and assistance for statistical planning and analyses. M. Ellison, has diverse and extensive experience in the design, conduct, and analysis of biomedical research projects. Services range in scope from simple consultations to more in-depth collaborations, depending on the nature of the required assistance:
- Study design - Consultation on statistical issues for new research projects (formulation of quantifiable hypotheses, identification of appropriate statistical methods to test hypotheses, and development of appropriate power and sample size calculations).
- Statistical analysis - Assistance with the conduct and interpretation of statistical analyses.
- Manuscript preparation - Editing of abstracts and manuscripts; development of graphics.
- General statistical consultation - Support in biostatistics and statistical genetics at all stages of the research process.
ID gene and pathway analysis: IDDRC investigators can use up to 20 hours consultation time/year free of charge. Additional time carries a fee of the hourly rate.
Microarray and HTS data analysis: Consultation and limited pilot analyses are free of charge. Most projects require large effort and, therefore, are charged at the hourly rate.
Statistics: IDDRC investigators can use up to 20 hours consultation time/year free of charge. Additional time carries a fee of the hourly rate.