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OpenHelix

An integrated view of gene structure and SNP variations

Tutorial and training materials by OpenHelix

Learn to use the GeneSNPs resource whose goal was to provide an integrated, gene-centric view of cDNA, genomic and SNP sequence information for human genes. This web resource was developed and maintained by the University of Utah Genome Center with funding from the National Institute of Environmental Health Sciences (NIEHS) as part of their Environmental Genome Project (EGP). This EGP web resource integrated gene, sequence and polymorphism data into individually annotated gene models. High quality and high density data are provided.
  • NOTE: The GeneSNPs resource is still available, but is no longer being maintained. GeneSNPs was last updated March of 2008. Our tutorial on this resource remains available for anyone wishing to use the GeneSNPs resource in its current state.
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You'll learn:

  • to perform text and sequence searches to find genes of interest
  • to understand the displays and data types available
  • to use the unique PDBViewer to examine SNPs in the context of protein structure

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  • Ye Olde Tutorials : These tutorials are those that are no longer being updated due to various reasons: the resource is not being updated or maintained any longer, is no longer licensed, etc. Some people may be running legacy copies, however. The materials are still useful and are offered to our users as an additional resource.

Recent BioMed Central research articles citing this resource

Matsui Katsuyuki et al., Combined effect of regulatory polymorphisms on transcription of UGT1A1 as a cause of Gilbert syndrome. BMC Gastroenterology (2010) doi:10.1186/1471-230X-10-57

Choudhury Ananya et al., Analysis of variants in DNA damage signalling genes in bladder cancer. BMC Medical Genetics (2008) doi:10.1186/1471-2350-9-69

Scheckenbach Kathrin et al., An intronic alteration of the fibroblast growth factor 10 gene causing ALSG-(aplasia of lacrimal and salivary glands) syndrome. BMC Medical Genetics (2008) doi:10.1186/1471-2350-9-114

Wjst Matthias et al., Target SNP selection in complex disease association studies. BMC Bioinformatics (2004) doi:10.1186/1471-2105-5-92

Dvornyk Volodymyr et al., Current limitations of SNP data from the public domain for studies of complex disorders: a test for ten candidate genes for obesity and osteoporosis. BMC Genetics (2004) doi:10.1186/1471-2156-5-4

More about the resource:

Although we now have an “official” human genome sequence, it is clear that understanding the variations among individuals is crucial to our understanding of human biology in health and disease susceptibility. And the interplay of our genetic background and the environment in which we live affects our health. To study this, the National Institute of Environmental Health Sciences (NIEHS) has created the Environmental Genome Project, or EGP. Formed in the late 1990s, this functional genomics effort has been yielding high quality data and tools for candidate genes of interest. GeneSNPs is one of the resources developed in support of the EGP for the scientific community.

Click here for technical information on using OpenHelix tutorial and training materials

The materials and slides offered can not be resold or used for profit purposes. Reproduction, distribution and/or use is strictly limited to instructional purposes only and can not be used for for monetary gain or wide distribution.
Copyright 2009, OpenHelix, LLC.

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