Pan-Omics and Data Science Core (PODS)

The Pan-Omics and Data Science Core (PODS) provides comprehensive and innovative support for study design, sample preparation, analysis, interpretation, and integration of a broad range of omics studies.

Core Services

Expertise in the design and implementation of a broad range of studies, including expertise on:

  • study design
  • technology platforms
  • sample preparation
  • other protocols

Sequencing and Bioinformatics services for genomics and epigenomics studies, including:

  • RNA-seq
  • ChIP-seq
  • microarrays
  • microRNA expression
  • Infinium MethylationEPIC BeadChip
  • Exome sequencing
  • ATAC-seq
  • reduced representation (RRBS) or whole-genome (WGBS) bisulfite sequencing
  • MeDIP-seq, MethylCap-seq, hmeDIP-seq, etc.
  • Enrichment testing (pathway analysis), and more

Assistance in publication and grant preparation (including P30 pilot proposals), data sharing, presentations (e.g., data visualization). ). Guidance for accessing Michigan Genomics Initiative data, a shared genomic resource at the University of Michigan.

PODS Resources

Provide genomic analysis resources for all Center-related projects. Researchers will have access to full services for epigenomics experiments; individual labs may submit cells for DNA/RNA extraction or ChIP-DNA for ChIP-Seq. The core will perform sample library preparation for the main DNA methylation platforms and sequencing applications, RNA-seq, or ChIP-seq. Prepared samples will be sent directly to the UM DNA Sequencing core, and generated data will be sent directly for bioinformatics service. In addition to the Epigenomics-related services described above, Center researchers can directly request access to technologies such as whole-genome sequencing, small RNA sequencing, microarrays, etc.

We will also make recommendations and help facilitate interactions with the BRCF UM DNA Sequencing Core, Metabolomics Core, Bioinformatics Core and Epigenomics Core

Pan-Omics and Data Science Education

PODS organizes workshops and seminars for environmental scientists and the broader biomedical community to learn more about current Pan-Omics and Data Science approaches. Our most recent workshop was a great success and offered ample time for networking among environmental health scientists. For example:

Classes and/or one-on-one consultations are available (see below, for resource details). Suggestions for future offerings are welcome. For more information, contact Maureen Sartor. Upcoming workshops offered through the Taubman Health Sciences Library can be found here: http://www.lib.umich.edu/taubman-health-sciences-library/workshops-and-instruction

Selected Tools & Resources

Cytoscape is an open source bioinformatics platform for visualizing molecular interaction networks and biological pathways and integrating these networks with annotations, gene expression profiles and other state data. The Cytoscape core distribution provides a basic set of features for data integration and visualization. Additional features are available as plugins. (http://www.cytoscape.org)
The MetScape plugin for Cytoscape provides a bioinformatics framework for the visualization and interpretation of metabolomic and gene expression profiling data, in the context of human metabolism. It allows users to build and analyze networks of genes and compounds, identify enriched pathways from expression profiling data, and visualize changes in metabolite data. (http://metscape.ncibi.org)
Need a tool to make biological sense of high-throughput data? GeneGo provides a commercial solution for using gene/protein/miRNA/RNA/drug/metabolite lists and “omics” data to generate and prioritize hypotheses. MetaCore is an integrated knowledge database and software suite for pathway analysis of experimental data and gene lists. The scope of data types includes microarray and sequence-based gene expression, SNPs and CGH arrays, proteomics, metabolomics, Co-IP pull-out and other custom interactions. ToxHunter is a systems toxicology knowledgebase and data analysis package, designed for the assessment of safety liabilities of drugs, environmental contaminants and other xenobiotics at all stages of discovery and development. CCMB has a license for use of GeneGo. (www.genego.com)
LRpath, RNA-Enrich and ChIP-Enrich
LRpath is a statistically powerful gene set enrichment testing method that can aid in interpreting high-throughput results, such as from gene expression or DNA methylation experiments (http://lrpath.ncibi.org). RNA-Enrich is a new method offered on the LRpath website, specifically for RNA-seq data. ChIP-Enrich is a website and Bioconductor package for gene set enrichment testing of ChIP-seq data (http://chip-enrich.med.umich.edu) or other large sets of genomic regions. It’s sister program, Broad-Enrich, is more useful for sets of broad genomic regions, such as those identified from ChIP-seq data assessing histone modifications (http://broad-enrich.med.umich.edu).
Gene2MeSH and Metab2MeSH
Gene2MeSH and Metab2MeSH use a statistical approach to reliably and automatically annotate genes or small compounds, respectively, with the concepts defined in Medical Subject Headings (MeSH). MeSH is the National Library of Medicine’s controlled vocabulary for biology and medicine, and includes diseases, phenotypes, environmental exposures and other chemicals, plus much more. (http://gene2mesh.ncibi.org and http://metab2mesh.ncibi.org)
iLINCS Web Portal
The integrative LINCS genomics data portal is an integrative computational platform for the analysis and mining of genomics datasets, signatures, compounds and genes. It is developed at the University of Cincinnati by a BIC external advisor, Dr. Mario Medvedovic. (http://ilincs.org/ilincs ). It is a useful resource especially for those studying the cells’ response to small molecules, drugs, or toxicogenomics.
Comparative Toxicogenomic Database (CTD)
CTD advances understanding of the effects of environmental chemicals on human health. CTD includes curated data describing cross-species chemical-gene/protein interactions and chemical- and gene-disease relationships to illuminate molecular mechanisms underlying variable susceptibility and environmentally influenced diseases. These data provide insights into complex chemical-gene and protein interaction networks. (http://ctd.mdibl.org)
GenePattern is a powerful genomic analysis platform developed at the Broad Institute. It provides access to more than 150 tools for gene expression, RNA-seq, proteomics, and SNP analysis; flow cytometry; and common data processing tasks. A web-based interface provides easy access to these tools and allows the creation of multi-step analysis pipelines that enable reproducible in silico research. (http://www.broadinstitute.org/genepattern)