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 Rv0628c/-:

update plot	correlation	link to info on gene
Rv3439c/-	(cc=0.4635)	info on Rv3439c/-
Rv1075c/-	(cc=0.4544)	info on Rv1075c/-
Rv2768c/PPE43	(cc=0.4372)	info on Rv2768c/PPE43
Rv0791c/-	(cc=0.4334)	info on Rv0791c/-
Rv3371/-	(cc=0.4293)	info on Rv3371/-
Rv2034/-	(cc=0.4255)	info on Rv2034/-
Rv2831/echA16	(cc=0.4153)	info on Rv2831/echA16
Rv2013/-	(cc=0.4142)	info on Rv2013/-
Rv2420c/-	(cc=0.4128)	info on Rv2420c/-
Rv2002/fabG3	(cc=0.4088)	info on Rv2002/fabG3

Correlation of Rv0628c/- with Rv2002/fabG3

Normalized LFCs for Rv0628c/-:
(description and provenance of datasets)

	Rv0628c/-	Rv2002/fabG3
Fe_supp_jason_reseq	-1.418	-0.428
low_pH_jason_reseq	-1.128	0.154
NO_jason_reseq	0.845	1.076
B6_jason_reseq	-0.181	0.253
MHCII_jason_reseq	-0.579	-0.136
Isoniazid02	0.503	1.014
Rifampicin4	0.474	-0.482
Ethambutol3	0.045	1.17
Meropenem3	0.483	0.254
Vancomycin16	0.098	0.08
Rv2680_day32	1.237	2.861
H37Rv_KO_MarP	0.319	0.154
hypoxia_3wks	0.159	0.459
hypoxia_6wks	0.01	-0.109
glycerol	-0.462	0.566
cholesterol	1.184	0.563
AJ	0.076	0.079
Bibs02	0.38	1.183
Bibs02c	-0.07	0.227
BL6	0.07	-0.121
BL6a	-0.344	0.067
BXD01	-0.431	-0.376
BXD010	-1.06	-0.724
BXD011	-0.415	-0.577
BXD03	-0.904	-0.875
BXD04	-0.095	0.014
BXD05	0.312	-0.33
BXD06	-0.151	-0.835
BXD07	0.365	-0.838
BXD08	0.179	-0.86
BXD09	-0.642	-0.189
CAST	0.479	0.521
CCcont	0.113	-1.206
DS01	0.741	1.251
DS02	0.849	0.121
DS04	1.952	1.439
DS0c	0.105	1.178
GP01	-0.458	0.107
GP02	-1.061	0.24
GP0c	-0.233	-0.158
NOD	-0.633	0.801
NZO	-0.874	-1.011
PWK	0.016	-0.658
H37Rv_KO_CtpC	-0.753	-0.95
H37Rv_KO_CtpD	-0.637	0.0
H37Rv_KO_Rv1272	-0.219	0.514
H37Rv_KO_SugABC	-1.277	-1.05
H37Rv_KO_MbtN	-0.546	-0.623
Trans05	-0.532	0.549
macrophage_unactivated	0.859	0.71
IL1	1.092	0.943
Rapamycin	1.08	-0.175
Tcell	0.388	0.0
GMCSF	1.354	0.995
IFNab	0.39	0.221
IFNg	-0.214	-0.206
IFNg_GMCSF1	-0.116	-0.562
Rv1432_day32	0.587	-0.648
Rv1565c_day32	1.205	-0.629
secA2_input	1.223	0.423
delta_Rv3594	0.828	0.814
delta_Rv3717	0.54	0.921
delta_Rv3811	2.085	1.599
delta_Rv0954	1.246	0.362
PonA1	1.503	-0.519
EccD1_KO	0.089	0.839
EspI_KO	0.02	0.211
PE35_KO	-1.485	1.041
PPE68_KO	-0.531	0.883
glycerol2	0.0	0.196
lignocerate	0.429	-0.402
oleate	-0.121	0.75
phosphatidylcholine	0.594	0.298
acetate	-0.171	-0.618
glucAc	-0.243	-1.292
Rv0950ko	0.069	-0.7
Rv1096ko	-0.069	0.392
Rv3684ko	-0.671	0.819
delta_otsA_trehalose	-0.925	-0.778