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 Rv0876c/-:

update plot	correlation	link to info on gene
Rv0016c/pbpA	(cc=0.5591)	info on Rv0016c/pbpA
Rv1821/secA2	(cc=0.5382)	info on Rv1821/secA2
Rv3207c/-	(cc=0.5306)	info on Rv3207c/-
Rv1565c/-	(cc=0.5271)	info on Rv1565c/-
Rv0867c/rpfA	(cc=0.5245)	info on Rv0867c/rpfA
Rv2176/pknL	(cc=0.5121)	info on Rv2176/pknL
Rv0050/ponA1	(cc=0.512)	info on Rv0050/ponA1
Rv1411c/lprG	(cc=0.51)	info on Rv1411c/lprG
Rv2922c/smc	(cc=0.5094)	info on Rv2922c/smc
Rv0260c/-	(cc=0.5065)	info on Rv0260c/-

Correlation of Rv0876c/- with Rv2176/pknL

Normalized LFCs for Rv0876c/-:
(description and provenance of datasets)

	Rv0876c/-	Rv2176/pknL
Fe_supp_jason_reseq	1.877	0.42
low_pH_jason_reseq	-0.793	0.315
NO_jason_reseq	0.15	0.617
B6_jason_reseq	-0.617	0.06
MHCII_jason_reseq	-0.922	-0.018
Isoniazid02	-0.681	-0.674
Rifampicin4	-0.872	-0.999
Ethambutol3	-2.067	-2.089
Meropenem3	0.779	-0.052
Vancomycin16	-1.005	-0.883
Rv2680_day32	-0.917	-0.51
H37Rv_KO_MarP	-3.914	-2.077
hypoxia_3wks	0.295	0.0
hypoxia_6wks	-0.614	0.142
glycerol	2.24	-0.373
cholesterol	1.282	0.21
AJ	-0.388	0.158
Bibs02	0.799	1.285
Bibs02c	-0.887	1.299
BL6	0.546	0.085
BL6a	-0.077	0.983
BXD01	0.274	0.368
BXD010	0.227	0.506
BXD011	0.68	0.26
BXD03	-0.109	-0.8
BXD04	0.508	0.1
BXD05	0.148	-0.47
BXD06	0.401	0.073
BXD07	0.375	-0.539
BXD08	0.321	0.637
BXD09	0.75	-0.146
CAST	-1.113	-0.312
CCcont	1.574	0.18
DS01	0.0	1.591
DS02	0.239	1.416
DS04	-0.325	2.264
DS0c	1.848	2.077
GP01	-0.363	1.011
GP02	-0.635	-0.359
GP0c	-1.22	-0.24
NOD	-0.825	0.843
NZO	-0.845	-0.058
PWK	-0.158	1.155
H37Rv_KO_CtpC	1.569	0.957
H37Rv_KO_CtpD	0.306	0.853
H37Rv_KO_Rv1272	0.651	0.808
H37Rv_KO_SugABC	1.071	0.92
H37Rv_KO_MbtN	1.17	0.302
Trans05	-0.344	1.104
macrophage_unactivated	0.511	0.546
IL1	0.572	-0.077
Rapamycin	0.497	-0.335
Tcell	0.0	0.251
GMCSF	0.887	-0.069
IFNab	1.097	-0.16
IFNg	0.898	1.09
IFNg_GMCSF1	0.314	-0.811
Rv1432_day32	0.213	-0.763
Rv1565c_day32	-0.199	0.0
secA2_input	-0.2	-0.377
delta_Rv3594	-0.26	0.545
delta_Rv3717	-1.067	0.39
delta_Rv3811	0.397	0.269
delta_Rv0954	-2.965	-1.368
PonA1	-1.924	-2.68
EccD1_KO	-0.072	0.457
EspI_KO	0.388	0.519
PE35_KO	-0.403	0.405
PPE68_KO	0.138	0.102
glycerol2	-0.213	0.241
lignocerate	0.044	0.449
oleate	-0.804	-1.664
phosphatidylcholine	-0.27	0.723
acetate	0.116	0.09
glucAc	0.0	0.161
Rv0950ko	0.163	-0.811
Rv1096ko	-1.601	-1.408
Rv3684ko	-0.704	-0.943
delta_otsA_trehalose	-1.336	0.158