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Genomatix Training—July 7 – 8

The NIH Library Bioinformatics Support Program is presenting a Genomatix training class July 7 – 8. The free training will be held in the NIH Library Training Room, Building 10, from 9:30 a.m. to 4:00 p.m. over two days.

Additionally, the bioinformatics workstation and training room has been reserved on July 11 from 9:30 a.m. – 4:00 p.m. for anyone who would like to schedule a consultation with a Genomatix representative to learn more about the software or answer any questions they may have.

Description
The Genomatix Software Suite allows detailed analysis of genomic and high-throughput data with a strong emphasis on understanding the molecular mechanisms of eukaryote gene regulation and expression. Genomatix provides tools and data content to thoroughly investigate the biology hidden in a gene or gene list, whether derived from a microarray experiment or Next Generation Sequencing (NGS). The Genomatix Software Suite provides fast and comprehensive analysis linking biological knowledge derived from the literature to the Genomatix collection of primary and expert-curated molecular sequence databases, including high-quality genomic annotation, promoters, transcripts, transcription factors and canonical pathway data. The integration of extensive data content and novel tools for visualization allow the researcher to obtain biological results quickly, based on an approach for merging multiple lines of evidence, all pointing to a common endpoint and in an easy-to-use and intuitive graphical user interface (GUI).

In this Core Seminar training course, students will learn how to use the Genomatix Portal interface to explore the comprehensive genome annotation, and to use it as a basis for:

  • Detailed promoter analyses
  • Predicting, analyzing and comparing transcription factor binding site patterns in genomic DNA
  • Defining new binding sites in genomic DNA
  • Analyzing the effects of single nucleotide polymorphisms (SNPs) on transcription factor binding sites

Objectives

Module 1: Genome Annotation: The Basis for Promoter Analysis
9:30 – 11:30 a.m., July 7

Introductory talk: From Genes to Networks, from Isolation to Context—Paradigms of Systems Biology and Systems Medicine

  • Search for genome annotation by keyword, sequence or genomic region
  • Upload and visualize genomic data in the Genome Browser
  • View the range of transcript and promoter annotations in ElDorado, including CAGE tag-based transcriptional start region annotation
  • Retrieve sequence and position data of annotated elements

Module 2: Transcription Factor (TF) Binding Site Analysis
1:00 – 4:00 p.m., July 7

Introductory talk: Genetic Predisposition: From Observation to Associated Regulatory Mechanisms

  • Predict conserved TF binding sites by comparative genomics
  • Analyze TF binding sites in genomic sequences
  • Perform a comparative TF binding site analysis
  • Create TF weight matrices and TF binding site definitions from ChIP-Seq data
  • Analyze the effects of single nucleotide polymorphisms (SNPs) on TF binding sites

Module 3: Functional Promoter Analysis
9:30 a.m. – 4:00 p.m., July 8

  • Generate a framework of TFBSs (e.g., in promoters), called Multiple Organized Regulatory Element cassette (MORE) from experimental data and search for potentially co-regulated genes
  • Search for evolutionarily conserved MORE-cassettes in promoters
  • Perform a comparative promoter analysis to define MORE-cassettes
  • Identify conserved regulatory elements in PromoterInspector Regions
  • Design promoters de novo

Benefits

  • Gain experience in quickly finding the most relevant genomic information for any gene(s) or genomic region
  • Learn how to quickly and efficiently analyze transcription factor binding site patterns in genomic DNA
  • Become proficient at carrying out a detailed analysis of promoters and promoter sets
  • Learn to detect functionally relevant promoter regions using MORE cassettes

Instructors
This class will be taught by Genomatix research staff:
Susan M. Dombrowski, Ph.D., Senior Support Scientist, Genomatix, Inc.
Thomas Werner, Ph.D., Founder of Genomatix, Inc.

Time Required

Registration for this class is no longer available.


Module 1: 9:30 a.m. – 11:30 a.m., July 7
Module 2: 1:00 p.m. – 4:00 p.m., July 7
Module 3: 9:30 a.m. – 4:00 p.m., July 8

Additionally, the bioinformatics workstation and training room has been reserved on July 11 from 9:30 a.m. – 4:00 p.m. for anyone who would like to schedule a consultation with a Genomatix representative.

Sign language interpreters and other reasonable accommodations can be provided. If you require such accommodations, please contact the NIH Library Information Desk at 301.496.1080 five business days in advance. For TDD users/callers, please call the above number through the Federal Relay Service at 1.800.877.8339.

The NIH Library in Building 10 serves the information needs of NIH staff and select Department of Health and Human Services (HHS) agencies. The NIH Library is part of the Office of Research Services (ORS) in the Office of the Director (OD).

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