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 Rv2662/-:

update plot	correlation	link to info on gene
Rv2911/dacB2	(cc=0.4301)	info on Rv2911/dacB2
Rv0516c/-	(cc=0.3774)	info on Rv0516c/-
Rv2148c/-	(cc=0.356)	info on Rv2148c/-
Rv1477/ripA	(cc=0.3539)	info on Rv1477/ripA
Rv3856c/-	(cc=0.3485)	info on Rv3856c/-
Rv1527c/pks5	(cc=0.3478)	info on Rv1527c/pks5
Rv1089/PE10	(cc=0.3455)	info on Rv1089/PE10
Rv0969/ctpV	(cc=0.3432)	info on Rv0969/ctpV
Rv0630c/recB	(cc=0.3416)	info on Rv0630c/recB
Rv1961/-	(cc=0.3411)	info on Rv1961/-

Correlation of Rv2662/- with Rv1527c/pks5

Normalized LFCs for Rv2662/-:
(description and provenance of datasets)

	Rv2662/-	Rv1527c/pks5
Fe_supp_jason_reseq	1.86	0.175
low_pH_jason_reseq	-0.547	-0.587
NO_jason_reseq	-0.05	-0.155
B6_jason_reseq	-0.057	0.181
MHCII_jason_reseq	-1.027	0.229
Isoniazid02	0.009	-0.015
Rifampicin4	-0.068	-0.057
Ethambutol3	-0.185	0.225
Meropenem3	-0.165	0.915
Vancomycin16	0.684	-0.056
Rv2680_day32	-0.228	-0.199
H37Rv_KO_MarP	0.862	0.189
hypoxia_3wks	-0.124	0.159
hypoxia_6wks	0.077	0.294
glycerol	-0.161	0.196
cholesterol	-0.61	0.013
AJ	0.844	0.622
Bibs02	0.984	0.15
Bibs02c	0.556	0.477
BL6	0.161	0.251
BL6a	0.818	0.066
BXD01	-0.368	-0.215
BXD010	0.495	0.021
BXD011	-0.021	-0.262
BXD03	0.093	-0.108
BXD04	-0.511	-0.508
BXD05	1.146	0.022
BXD06	0.218	-0.39
BXD07	-0.015	-0.036
BXD08	0.065	0.022
BXD09	0.293	-0.304
CAST	-1.086	-0.12
CCcont	0.127	0.025
DS01	0.84	0.554
DS02	1.084	0.126
DS04	2.195	0.455
DS0c	0.343	0.325
GP01	3.083	1.712
GP02	0.266	0.477
GP0c	1.181	0.555
NOD	-1.261	0.304
NZO	1.932	0.314
PWK	0.033	-0.017
H37Rv_KO_CtpC	0.683	0.314
H37Rv_KO_CtpD	-0.414	0.143
H37Rv_KO_Rv1272	0.127	0.415
H37Rv_KO_SugABC	0.865	0.611
H37Rv_KO_MbtN	1.546	-0.13
Trans05	-0.823	0.289
macrophage_unactivated	1.272	-0.158
IL1	0.724	-0.074
Rapamycin	-0.853	-0.114
Tcell	0.274	-0.081
GMCSF	-0.671	0.19
IFNab	0.889	-0.151
IFNg	0.224	-0.134
IFNg_GMCSF1	1.04	0.189
Rv1432_day32	0.0	0.216
Rv1565c_day32	-1.657	-0.104
secA2_input	0.299	0.523
delta_Rv3594	0.642	0.021
delta_Rv3717	0.922	-0.374
delta_Rv3811	0.916	0.312
delta_Rv0954	0.129	-0.172
PonA1	-0.669	0.492
EccD1_KO	0.52	0.089
EspI_KO	0.111	0.262
PE35_KO	1.698	0.23
PPE68_KO	2.262	0.378
glycerol2	0.193	0.46
lignocerate	1.019	0.673
oleate	-2.066	0.373
phosphatidylcholine	0.258	0.696
acetate	0.289	0.845
glucAc	0.333	0.441
Rv0950ko	0.844	0.422
Rv1096ko	1.858	0.311
Rv3684ko	1.611	0.498
delta_otsA_trehalose	0.957	0.551