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HSLS MolBio Workshops

Information & resources for hands-on bioinformatics classes.

Objective

This workshop provides an overview of resources and search strategies on transcriptional regulation. Emphasis will be given to HSLS-licensed TRANSFAC/Match and Correlation Engine software, as well as open-access tools such as the UCSC genome browser and Cistrome data browser

Participants will learn to

  • retrieve information linked with a transcription factor
  • retrieve the promoter sequence for a gene of interest
  • extract transcription regulatory elements--promoters, enhancers, and silencers associated with a gene of interest
  • identify the transcription factor binding site(s) present in a DNA sequence
  • identify transcription factor binding sites present in a ChIP-Seq dataset (motif discovery)
  • identify upstream regulatory transcription factors for a differentially expressed gene data set
  • start with a gene expression data set and find correlated studies with gene perturbation experiments (knock-out, knock-down, etc.) available in the GEO database
  • start with a ChIP-Seq data set and find factors that have a significant binding overlap with the ChIP-Seq peak set

Target Audience

Experimental biologists seeking to analyze bulk RNA-Seq data generated through experiments or retrieved from a repository such as GEO. The software covered in the workshop operates through a user-friendly, point-and-click graphical user interface, so neither programming experience nor familiarity with the command-line interface is required.

Workshop Materials

Powerpoint

Lecture Video

  • Part1 - morning session offered on February 03, 2021
  • Part2 - afternoon session offered on February 03, 2021

Data Download

  • Myc_human - generic promoter sequence for human myc
  • CD274_human - generic promoter sequence for CD247
  • RUNX1_ChIPseq - RUNX1 transcription factor binding peaks in .bed format
  • AI-10-49 vs DMSO RNA_Seq - differentially expressed genes between AI-10-49 treatment vs. DMSO (control) formatted for IPA upload
  • AI-10-49 vs DMSO RNA-seq - differentially expressed genes between AI-10-49 treatment vs. DMSO (control) formatted for Correlation Engine upload
  • Practice Exercise (SARSCov-2 vs mock_Calu3) - a dataset with the differentially expressed genes between SARS-CoV2 infected vs. mock-infected Calu3 cells for practice
  • CD47_UCSCGB - UCSC Browser displaying  Myc binding sites on CD47 promoter region 

Software Registration

Databases and Tools

  • GeneExplain Portal - provides bioinformatics, systems biology, and cheminformatics software and databases for life science and medical research.
  • UCSC Genome Browser 
  • UCSC GB_CD47 - UCSC genome browser displaying CD47 promoter sequence
  • BLAT - Paste in a query sequence to find its location in the genome.
  • Jasper - contains a curated, non-redundant set of profiles, derived from published and experimentally defined transcription factor binding sites for eukaryotes. 
  • GeneCards - a searchable, integrative database that provides comprehensive, user-friendly information on all annotated and predicted human genes. 
  • Cistrome Data Browser - Check what factors regulate your gene of interest, what factors bind in your interval or have a significant binding overlap with your peak set.
  • Cistrome ToolKit - allows users to quickly examine their hypothesis regarding gene regulation through public ChIP-seq (protein factors and histone marks), chromatin accessibility (DNase-seq and ATAC-seq) data.
  • Illumina Correlation Engine - support research to identify mechanisms of disease, drug targets, and prognostic or predictive biomarkers.
  • BioRender - Scientific illustrations creating tool

References

Publications citing GeneXplain/Biobase/Transfac from Pitt researchers

 

Attribution

Please include the following statement in the acknowledgments section for all publications, posters, and presentations: 

[Software name] licensed through the Molecular Biology Information Service of the Health Sciences Library System, University of Pittsburgh was used for data analysis.

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