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Tutorial for Nichols et al. (2011) chemical genomics data

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Nichols et al. (2011)[1] determined quantitative growth scores for xx E. coli mutants in 324 conditions covering 114 unique stresses. The xx mutants tested included Keio single gene deletions[2]; essential gene hypomorphs (C-terminally tandem-affinity tagged[3] or specific alleles); and a set of small RNA/small protein knockouts[4]. The results from this study are available for browsing or download at porteco.org.

Contents

Browsing the data

(1) Start on the PortEco Home Page at porteco.org

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(2) Click on "Browse All Data"

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(3) You can browse either Strains Or Conditions

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(4) To find conditions that affect the fitness of a particular mutant

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(5) Partial list of conditions that where marR(del) has reduced fitness

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(6) You can search for other mutants that have reduced fitness under the same conditions as marR(del)

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(7) Partial list of mutants that are correlated with marR(del)

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(8) You can also search for conditions that have similar effects

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(9) Partial list of conditions that are correlated with Procaine 10

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References

  1. Baba, T et al. (2006) Construction of Escherichia coli K-12 in-frame, single-gene knockout mutants: the Keio collection. Mol. Syst. Biol. 2 2006.0008 PubMed EcoliWiki page
  2. Butland, G et al. (2005) Interaction network containing conserved and essential protein complexes in Escherichia coli. Nature 433 531-7 PubMed EcoliWiki page
  3. Hobbs, EC et al. (2010) Small RNAs and small proteins involved in resistance to cell envelope stress and acid shock in Escherichia coli: analysis of a bar-coded mutant collection. J. Bacteriol. 192 59-67 PubMed EcoliWiki page