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Genome Regulation
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TOOLS and RESOURCES

Gene Expression Viewer

  • GE Viewer is visualization tool to look up gene expression profiles in different conditions.

TranscriptomeViewer

  • pombeTV is a tool for displaying tiling chip and next-generation sequencing data for genomic regions.

PInt

  • PInt (Pombe Interactome) is a tool that allows you to retrieve predictions of fission yeast protein interactions, based on more than 100 features of the proteins.


YOGY: eukarYotic OrtholoGY

  • YOGY is an integrated resource to search for orthologous proteins in 11 organisms.



PPPP: Pombe PCR Primer Programs

Web-interface scripts to design primers for PCR-based gene targeting in S. pombe

  • Gene Deletion

  • C-terminal tagging

  • Get primers for controlling genes by nmt promoter and/or N-terminal tagging

These scripts have been described in:
Penkett and Bähler (2006). Simplified primer design for PCR-based gene targeting and microarray primer database: two web tools for fission yeast.
Yeast 23:921-928.

Microarray Data

  • Meta-analysis
  • Meiotic differentiation
  • Stress Responses
  • Cell Cycle
  • Other Projects

Protocols

  • Protocols we use for microarray experiments.

Presentations

  • Presentations available as PDF files.

Other scripts

These scripts are for primer design and initial microarray data processing and are available as .zip files:

  • Initial microarray data processing (data filtering, local normalisation and quality control)

  • Intragenic Microarray Primer design

  • Intergenic Microarray Primer design

These scripts have been described in:
Lyne R, Burns G, Mata J, Penkett CJ, Rustici G, Chen D, Langford C, Vetrie D, and Bähler J (2003). Whole-genome microarrays of fission yeast: characteristics, accuracy, reproducibility, and processing of array data.
BMC Genomics 4:27 (PDF).

Microarray Primer Database

  • Primer Database to retrieve the sequences and accompanying information for primers and PCR products used for our in-house arrays.

This database has been described in:
Penkett and Bähler (2006). Simplified primer design for PCR-based gene targeting and microarray primer database: two web tools for fission yeast.
Yeast 23:921-928.