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Gene Regulation: Home

Overview

This hands-on workshop provides an overview of resources and search strategies on transcriptional regulation. Emphasis will be given to databases, including TRANSFAC (transcription factors), Proteome (promoter sequences) and RegulomeDB (SNPs with known and predicted regulatory elements). Software that will be covered: BIOBASE Match to locate transcription factor binding sites present in a query sequence, UCSC Genome Browser to visualize the regulatory regions present in the human genome generated by the Encyclopedia of DNA Elements (ENCODE) project, and the HSLS licensed tool – NextBio Enterprise to mine microarray/RNA Seq data from the Gene Expression Omnibus (GEO) repository.

 

 

Software

Workshop Content

 Participants will learn to

  1. retrieve promoter sequences
  2. determine transcription factor occupancy
  3. browse through the epigenetic biochemical markers
  4. start with a GEO  data set and find correlated studies using Correlation Engine 

Citations

Citing HumanPSD and GPCR-PD

Authors wishing to cite HumanPSD or GPCR-PD should use the following reference:

  • Hodges PE, Carrico PM, Hogan JD, O'Neill KE, Owen JJ, Mangan M, Davis BP, Brooks JE, Garrels JI. (2002) Annotating the human proteome: the Human Proteome Survey Database (HumanPSD) and an in-depth target database for G protein-coupled receptors (GPCR-PD) from Incyte Genomics. Nucleic Acids Research 30: 137-141. [Abstract]

 

Citing YPD, PombePD, WormPD, and MycoPathPD

Authors wishing to cite YPD, PombePD, WormPD, and MycoPathPD should use the following references:

  • Csank C, Costanzo MC, Hirschman J, Hodges P, Kranz JE, Mangan M, O'Neill K, Robertson LS, Skrzypek MS, Brooks J, Garrels JI. (2002) Three yeast proteome databases: YPD, PombePD, and CalPD (MycoPathPD). Methods Enzymol 350: 347-73. [Abstract]
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  • Costanzo MC, Hogan JD, Cusick ME, Davis BP, Fancher AM, Hodges PE, Kondu P, Lengieza C, Lew-Smith JE, Lingner C, Roberg-Perez KJ, Tillberg M, Brooks JE, Garrels JI. (2000) The yeast proteome database (YPD) and Caenorhabditis elegans proteome database (WormPD): comprehensive resources for the organization and comparison of model organism protein information. Nucleic Acids Res 28(1):73-6. [Abstract]

Contact Information

Ansuman Chattopadhyay's picture
Ansuman Chattopadhyay
Contact:
Ansuman Chattopadhyay, PhD
Head, Molecular Biology Information Service
Health Sciences Library System
University of Pittsburgh
412-648-1297
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