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Column_Key.md

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Key for standard SGA file formats.

Newer formats should have a header. Several alternative formats were 'standard' for a short while, but didn't survive and are not described here.

Conveniently, these all have a unique number of columns

  • 9 Cols: Database dump, input to compute_sgascore.m
  • 11 Cols: Final format of 2016 paper
  • 12 Cols: Output of compute_sgascore.m
  • 13 Cols: Final format of 2010 paper

INPUT to compute_sgascore.m

(rawdata from database)

9 col

  1. Query Orf
  2. Array Orf
  3. Array plate num (e.g. 354)
  4. Set ID
  5. Unique plate ID
  6. Batch ID
  7. row (1 : 32)
  8. column (1 : 48)
  9. colony_size (in pixels)

OUTPUT of compute_sgascore.m

(scored raw data)

12 col

  1. Query Orf
  2. Array Orf
  3. e_score*
  4. e_score (std)
  5. p-value
  6. Query smf
  7. Query smf (std)
  8. Array smf
  9. Array smf (std)
  10. Expected dmf
  11. Observed dmf
  12. Observed dmf (std)

* this file does not contain epsilon, but e_scores instead. You can calculate epsilon from this file as follows:

eps = Observed_dmf - Expected_dmf

Final format for 2016 paper

11 col

  1. Query Strain ID
  2. Query allele name
  3. Array Strain ID
  4. Array allele name
  5. Arraytype/Temp
  6. Genetic interaction score (ε)
  7. P-value
  8. Query single mutant fitness (SMF)
  9. Array SMF
  10. Double mutant fitness
  11. Double mutant fitness standard deviation

Final format for the 2010 paper

13 col

  1. Query ORF
  2. Query gene name
  3. Array ORF
  4. Array gene name
  5. Genetic interaction score (eps)
  6. Standard deviation
  7. p-value
  8. Query single mutant fitness (SMF)
  9. Query SMF standard deviation
  10. Array SMF
  11. Array SMF standard deviation
  12. Double mutant fitness
  13. Double mutant fitness standard deviation

Assignment file for score_trigenic_interactions.m

8 col

  1. StrainID1: strain ID of the first single mutant.
  2. ORF1: ORF of the first single mutant.
  3. StrainID2: strain ID of the second single mutant.
  4. ORF2: ORF of the second single mutant.
  5. DMstrainID: strain ID for the double mutant query (ORFs are ORF1 and ORF2).
  6. SM1strainID: strain ID for the single mutant (one of the ORFs will be YDL227C/HO).
  7. SM2strainID: strain ID for the other single mutant.
  8. Annotation: which class this interaction should be assigned to.

Output of print_trigenic.m

6 col

  1. Query Strain ID
  2. Array Strain ID
  3. Adjusted genetic interaction score (epsilon or tau)
  4. P-value
  5. Double/triple mutant fitness
  6. Double/triple mutant fitness standard deviation