Appendix

We detail the descriptions to each column of the simulated output datasets on this page.

Abbreviations

KO, knockout; SKO, single knockout; DKO, double knockout; %, percentage; GI, genetic interaction; std. dev., standard deviation.

Column descriptions of Simulated Datasets

  • guide_id: Unique guide ID by numerical order.

  • gene_pair_id: Target gene-pair ID.

  • gene1_gene2_id: ID of 1st target KO gene and 2nd target KO gene, separated by “_”. Any combination with 0 indicates it is SKO. For example,”1_2” indicates we are knocking out gene-pair targeting gene#1 and gene#2; and “1_0” indicates we knockout out gene#1 only.

  • guide1_id: ID of 1st target KO gene with corresponding guide, separated by “_”.

  • guide2_id: ID of 2st target KO gene with corresponding guide, separated by “_”.

  • construct_id: ID of constructs, containing information for both DKO gene and guide; 1st and 2nd KO target are separated by “__”. For example,”1_2__6_3” indicates a construct with 1st target on gene#1 and its second guide targeting it, combined with 2nd target on gene#6 and its third guide targeting it.

  • gene1: ID of 1st target KO gene.

  • gene2: ID of 2nd target KO gene.

  • guide1_eff: Guide-Efficacy of the guide targeting 1st KO gene.

  • guide2_eff: Guide-Efficacy of the guide targeting 2nd KO gene.

  • p1: Theoretical phenotype of 1st KO gene.

  • p2: Theoretical phenotype of 2nd KO gene.

  • p1i: Theoretical phenotype of 1st KO gene, with GI effects.

  • p2i: Theoretical phenotype of 2nd KO gene, with GI effects.

  • p1p: Theoretical phenotype of 1st KO gene, with guide-efficacy effects.

  • p2p: Theoretical phenotype of 2nd KO gene, with guide-efficacy effects.

  • p1ip: Theoretical phenotype of 1st KO gene, with both GI and guide-efficacy effects.

  • p2ip: Theoretical phenotype of 2nd KO gene, with both GI and guide-efficacy effects.

  • KO_type: Knockout type, whether this construct is SKO or DKO.

  • gene1_behavior: Gene class category for 1st KO gene.

  • gene2_behavior: Gene class category for 2nd KO gene.

  • i_interaction: Indicator for GI presence, 1 indicates there is GI, 0 indicates not.

  • interaction_gene: Gene-level interaction values. (simulated GI truth)

  • interaction_guide: Guide-level interaction values. (for records only, not practically used)

  • interaction_gene_type: Category of GI on whether there is none, negative, or positive GI presence.

  • interaction_guide_type: Category of GI on whether there is none, negative, or positive GI presence, on guide-level. (for records only, not practically used)

  • p0y_0: Probability of cell with no division and dies, without considering GI effects.

  • p1y_0: Probability of cell with 1 division, without considering GI effects.

  • p2y_0: Probability of cell with 2 divisions, without considering GI effects.

  • p3y_0: Probability of cell with 3 divisions, without considering GI effects.

  • p0y: Probability of cell with no division and dies, with GI effects.

  • p1y: Probability of cell with 1 division, with GI effects.

  • p2y: Probability of cell with 2 divisions, with GI effects.

  • p3y: Probability of cell with 3 divisions, with GI effects.

  • p0y_p0: Probability of cell with no division and dies, with guide-efficacy effects but not GI.

  • p1y_p0: Probability of cell with 1 division, with guide-efficacy effects but not GI.

  • p2y_p0: Probability of cell with 2 divisions, with guide-efficacy effects but not GI.

  • p3y_p0: Probability of cell with 3 divisions, with guide-efficacy effects but not GI.

  • p0y_p: Probability of cell with no division and dies, with both GI and guide-efficacy effects.

  • p1y_p: Probability of cell with 1 division, with both GI and guide-efficacy effects.

  • p2y_p: Probability of cell with 2 divisions, with both GI and guide-efficacy effects.

  • p3y_p: Probability of cell with 3 divisions, with both GI and guide-efficacy effects.

  • freq_t0: Frequency of the target gene-pair at initial timepoint.

  • rel_freq_t0: Relative abundance (frequency) of the target gene-pair at initial timepoint.

  • guide1_type: Indicator on type of the guide for 1st KO gene. (1 indicates high-efficacy guides, 0 indicates low-efficacy guides).

  • guide2_type: Indicator on type of the guide for 2nd KO gene. (1 indicates high-efficacy guides, 0 indicates low-efficacy guides).

  • freq_guide_t0: Frequency of the construct at initial timepoint.

  • counts_guide_t0: Counts of the construct at initial timepoint.

  • counts_guide_t1: Counts of the construct at the intermediate stage of cell growth and selection.

  • rel_freq_guide_t0: Relative abundance (frequency) of the construct at initial timepoint.

  • counts_guide_t2: Counts of the construct at final timepoint.

  • rel_freq_guide_t2: Relative abundance (frequency) of the construct at final timepoint.

  • LFC: Log2-Fold-Change of relative abundance from the construct at final vs. initial timepoint.