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 Rv3864/espE:

update plot	correlation	link to info on gene
Rv2179c/-	(cc=0.7226)	info on Rv2179c/-
Rv2569c/-	(cc=0.7148)	info on Rv2569c/-
Rv0502/-	(cc=0.6569)	info on Rv0502/-
Rv3050c/-	(cc=0.6401)	info on Rv3050c/-
Rv1633/uvrB	(cc=0.6342)	info on Rv1633/uvrB
Rv2190c/-	(cc=0.6272)	info on Rv2190c/-
Rv0642c/mmaA4	(cc=0.6243)	info on Rv0642c/mmaA4
Rv2584c/apt	(cc=0.6219)	info on Rv2584c/apt
Rv0929/pstC2	(cc=0.6216)	info on Rv0929/pstC2
Rv0930/pstA1	(cc=0.6206)	info on Rv0930/pstA1

Correlation of Rv3864/espE with Rv2584c/apt

Normalized LFCs for Rv3864/espE:
(description and provenance of datasets)

	Rv3864/espE	Rv2584c/apt
Fe_supp_jason_reseq	-0.532	-0.227
low_pH_jason_reseq	3.42	0.565
NO_jason_reseq	-0.69	0.404
B6_jason_reseq	-1.402	-0.929
MHCII_jason_reseq	-1.234	-1.215
Isoniazid02	-0.39	-0.808
Rifampicin4	-0.203	-0.146
Ethambutol3	0.142	-0.59
Meropenem3	0.768	-0.443
Vancomycin16	0.191	-0.268
Rv2680_day32	-0.228	0.892
H37Rv_KO_MarP	-2.191	-0.556
hypoxia_3wks	-0.371	0.738
hypoxia_6wks	-0.263	1.046
glycerol	0.709	0.758
cholesterol	0.614	-0.069
AJ	0.0	0.81
Bibs02	0.0	1.106
Bibs02c	0.887	0.932
BL6	2.486	0.958
BL6a	2.131	1.499
BXD01	2.047	0.868
BXD010	1.598	1.16
BXD011	1.811	0.701
BXD03	0.664	1.101
BXD04	1.854	1.281
BXD05	1.878	1.845
BXD06	2.59	1.349
BXD07	1.003	1.389
BXD08	1.781	1.048
BXD09	2.036	1.278
CAST	0.0	0.576
CCcont	3.145	1.444
DS01	1.001	0.274
DS02	0.764	0.12
DS04	1.689	-0.471
DS0c	0.596	0.511
GP01	1.35	0.774
GP02	0.159	0.966
GP0c	1.072	1.337
NOD	0.225	-0.042
NZO	0.0	0.407
PWK	0.831	0.658
H37Rv_KO_CtpC	0.571	0.281
H37Rv_KO_CtpD	1.044	1.793
H37Rv_KO_Rv1272	2.149	1.014
H37Rv_KO_SugABC	3.545	1.26
H37Rv_KO_MbtN	2.695	0.707
Trans05	2.677	1.018
macrophage_unactivated	2.228	0.619
IL1	-0.736	0.697
Rapamycin	0.651	0.893
Tcell	2.3	0.228
GMCSF	0.89	2.017
IFNab	1.197	0.931
IFNg	-0.663	-0.013
IFNg_GMCSF1	1.059	0.264
Rv1432_day32	-0.664	0.374
Rv1565c_day32	0.182	0.041
secA2_input	-1.387	-1.75
delta_Rv3594	0.962	0.347
delta_Rv3717	1.328	-0.422
delta_Rv3811	0.87	-0.207
delta_Rv0954	-0.615	-0.433
PonA1	-1.937	-0.406
EccD1_KO	-1.694	-0.977
EspI_KO	-2.718	-0.436
PE35_KO	0.0	-0.688
PPE68_KO	0.077	-0.611
glycerol2	0.028	0.378
lignocerate	-0.296	0.226
oleate	-0.801	0.55
phosphatidylcholine	-0.515	0.378
acetate	-0.364	0.484
glucAc	0.286	-0.133
Rv0950ko	-1.375	-0.703
Rv1096ko	-0.184	-0.401
Rv3684ko	-0.982	-1.117
delta_otsA_trehalose	0.366	-0.167