TnSeqCorr

• These are correlations of TnSeq responses across 82 experimental conditions.
• LFCs (log2-fold-changes) were computed for each gene in each condition relative to a relevant control condition (e.g. H37Rv grown on 7H9).
• The LFCs were normalized by dividing by the standard deviation for each condition. (so roughly, |LFC|>2 are the outliers, i.e. tails of the distribution)
• Note that essential genes often have LFCs around 0.
• Data for some genes is not available if they have less than 3 TA sites, or the dynamic range of LFCs is less than 2.0 across all conditions. (This is the case for many essential genes.)
• 'leverage' on each plot is a statistical score that indicates how much the regression is influenced by a few outlier points; the traditional threshold is indicated on the plots (3p/n, which is about 0.07 for this dataset), but in practice, cases with leverage > ~0.2 seem to be the least reliable (most misleading) correlation coefficients.

Top 10 genes with highest correlation to Rv1752/-:

update plot	correlation	link to info on gene
Rv1616/-	(cc=0.6756)	info on Rv1616/-
Rv1059/-	(cc=0.6077)	info on Rv1059/-
Rv0766c/cyp123	(cc=0.5917)	info on Rv0766c/cyp123
Rv1116/-	(cc=0.5785)	info on Rv1116/-
Rv3125c/PPE49	(cc=0.5649)	info on Rv3125c/PPE49
Rv1521/fadD25	(cc=0.5647)	info on Rv1521/fadD25
Rv3533c/PPE62	(cc=0.5595)	info on Rv3533c/PPE62
Rv0844c/narL	(cc=0.5574)	info on Rv0844c/narL
Rv1386/PE15	(cc=0.5481)	info on Rv1386/PE15
Rv1551/plsB1	(cc=0.5462)	info on Rv1551/plsB1

Correlation of Rv1752/- with Rv3533c/PPE62

Normalized LFCs for Rv1752/-:
(description and provenance of datasets)

	Rv1752/-	Rv3533c/PPE62
Fe_supp_jason_reseq	0.898	0.068
low_pH_jason_reseq	-0.161	-0.637
NO_jason_reseq	-0.764	-0.856
B6_jason_reseq	-0.729	0.508
MHCII_jason_reseq	-0.549	0.136
Isoniazid02	-0.434	0.124
Rifampicin4	0.555	0.133
Ethambutol3	1.171	0.623
Meropenem3	0.194	-0.19
Vancomycin16	0.0	0.066
Rv2680_day32	-2.199	0.363
H37Rv_KO_MarP	0.524	0.535
hypoxia_3wks	2.444	0.263
hypoxia_6wks	2.717	-0.297
glycerol	1.779	0.537
cholesterol	0.643	0.13
AJ	1.076	0.36
Bibs02	0.404	0.25
Bibs02c	-1.94	0.229
BL6	1.559	0.477
BL6a	2.314	0.769
BXD01	3.174	0.439
BXD010	1.471	0.233
BXD011	2.332	-0.041
BXD03	2.639	0.258
BXD04	3.421	1.225
BXD05	3.019	0.679
BXD06	3.229	0.158
BXD07	2.882	0.558
BXD08	2.391	0.321
BXD09	2.702	0.744
CAST	0.779	0.459
CCcont	1.774	0.259
DS01	-1.437	-0.024
DS02	-0.989	-0.343
DS04	-0.544	-0.282
DS0c	0.368	-0.264
GP01	2.24	0.559
GP02	3.888	1.043
GP0c	2.7	0.457
NOD	-0.142	0.408
NZO	1.621	1.475
PWK	0.117	0.215
H37Rv_KO_CtpC	2.829	0.432
H37Rv_KO_CtpD	1.947	0.368
H37Rv_KO_Rv1272	1.77	0.693
H37Rv_KO_SugABC	2.44	0.702
H37Rv_KO_MbtN	1.34	0.052
Trans05	-0.315	1.107
macrophage_unactivated	1.073	0.748
IL1	0.234	-0.362
Rapamycin	1.197	-0.184
Tcell	2.587	-0.398
GMCSF	0.504	0.269
IFNab	-0.577	-0.333
IFNg	-0.796	-0.759
IFNg_GMCSF1	-0.346	0.421
Rv1432_day32	0.18	0.576
Rv1565c_day32	-1.777	-0.461
secA2_input	0.44	0.402
delta_Rv3594	0.646	-1.049
delta_Rv3717	-0.608	-1.037
delta_Rv3811	-0.802	-0.349
delta_Rv0954	1.056	-0.824
PonA1	-0.6	-0.71
EccD1_KO	0.842	0.513
EspI_KO	0.625	0.2
PE35_KO	1.808	0.233
PPE68_KO	1.414	0.163
glycerol2	-0.336	-0.68
lignocerate	-1.251	-0.877
oleate	0.043	-0.099
phosphatidylcholine	-0.319	-0.443
acetate	-2.123	-0.768
glucAc	-1.959	-0.673
Rv0950ko	0.142	-0.19
Rv1096ko	1.131	-0.389
Rv3684ko	-0.976	-0.851
delta_otsA_trehalose	-2.184	-0.918