Genomatix Software Suite: Transcription Factor Binding Site and Promoter Analysis
Description:
The Genomatix Software Suite allows the detailed analysis of genomic data with a strong emphasis on understanding the molecular mechanisms of eukaryote gene regulation and expression. Whether your point of entry is a single gene or several thousand, the Genomatix Software Suite 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 a fast and comprehensive analysis linking biological knowledge derived from the literature to our collection of primary and expert-curated molecular sequence databases. These databases include (but are not limited to) high-quality genomic annotation, promoters, transcripts, transcription factors and canonical pathway data. The integration of our extensive data content and novel tools for visualization allow the researcher to obtain biological results quickly, based on our 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 our 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; and analyzing the effects of single nucleotide polymorphisms (SNPs) on transcription factor binding sites, to name just a few of the many possibilities available in our robust software environment.
Note: Instructional material will be taught in three parts, each of which is also suitable as a standalone module: Module 1 is 9:30 AM - 11:30 AM; Module 2 is 1:00 PM - 3:00 PM; and Module 3 is 3:00 PM - 5:00 PM.
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Formats for Training:
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Class
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Hands-on. Free. NIH and HHS staff only. NIH staff can register above. HHS staff can email a request to attend the class. Space is limited and registration is required.
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Objectives:
Students will learn in: Module 1: Genome Annotation: The basis for promoter analysis
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
Predict functional 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
Generate a promoter framework from experimental data and search for potentially co-regulated genes;
Search for evolutionarily-conserved models in promoters;
Perform a comparative promoter analysis;
Identify conserved regulatory elements in PromoterInspector Regions;
Perform gene ontology classification of TF binding site-specific promoters;
Design promoters de novo
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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
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Who Should Attend:
NIH staff interested in a biologist-oriented complete analysis and database package for understanding eukaryotic gene regulation and expression.
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