This data browser is for data from Nichols et al. (2010) Phenotypic Landscape of a Bacterial Cell. Cell 143, 1097–1109

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Growth data (Strain/Condition)
Correlations among strains
Correlations among conditions
strain Please enter at least one query.
If you leave a field empty, the search will look for all.
condition


item 1: ECK2208 => strain(s):' ECK2208'
item 2: => cond(s):all
.
strain cond score

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Enter a search term for a strain or condition in one or both of the input fields. If you leave one blank, the database will look for all values. The all x all arrays are very large, so we don't allow them to be displayed. The full datasets are available upon request.

Strains

The experiments were done with a combination of strains:

  • the Keio single gene deletion library (Babu et al., 2009)and a small RNA/small protein knockout library (Hobbs et al., 2010).
  • hypomorphs of essential genes [both C-terminally tandem-affinity tagged essential genes (Butland et al., 2005) and specific alleles were used];
  • a small RNA/small protein knockout library (Hobbs et al., 2010)

Note that the strain search looks for a match to the search string anywhere in the Gene nomenclature table. This allows you to search for a gene name, part of a product description, synonyms, or accessions. However, this can have unexpected consequences. For example:

  • Searching for "mal" will give all the ribosomal proteins.
  • Searching for "rpoS" will not only give the strain with rpoS deleted, it will also return strains that match based on gene descriptions containing rpoS

To make the search more specific, use an accession, such as an ECK number.

Conditions

The experiments were done on 324 conditions, including plating at different temperatures, at different pH, and with different chemical additions.

Searching for conditions will look for a match between your query and any part of the condition name. For example:

  • Searching for "acid" will give conditions with Fusidic acid or Naladixic acid.
  • Searching for "amp" will give conditions with ampicillin, Chloramphenicol or Rifampicin.
Some unexpected search results might occur due to the absence of spaces in the condition names. In addition, there are several precalculated lists of conditions:
  • "temperature" will return conditons listed by temperature
  • "pH" will return conditions based on pH.

Score

The score reflects a given strain's relative fitness under the corresponding conditions. Negative scores indicate a loss of fitness associated with deletion of a given gene under a given condition, while positive scores indicate a fitness gain. In general, higher magnitude scores correspond to more severe fitness changes

Download data files

coli_FinalData2.txt 12.3 MbTab delimited text file of correlation coefficients for strain x condition relative fitness scores
strainCC.txt 150.6 MbTab delimited text file of correlation coefficients for strain x strain profile comparisons
324drugCC.txt 1 MbTab delimited text file of correlation coefficients for condition x condition profile comparisons
conditions.txt 33 kbTab delimited text file of conditions and keywords
nichols.tgz 61.5 MbCompressed archive of the .txt files above
nichols.zip 61.5 Mb