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 Rv3576/lppH:

update plot	correlation	link to info on gene
Rv0140/-	(cc=0.4595)	info on Rv0140/-
Rv0944/-	(cc=0.4545)	info on Rv0944/-
Rv3528c/-	(cc=0.426)	info on Rv3528c/-
Rv0282/eccA3	(cc=0.419)	info on Rv0282/eccA3
Rv0055/rpsR1	(cc=0.4133)	info on Rv0055/rpsR1
Rv3706c/-	(cc=0.4068)	info on Rv3706c/-
Rv0397A/-	(cc=0.4058)	info on Rv0397A/-
Rv2751/-	(cc=0.4057)	info on Rv2751/-
Rv2497c/bkdA	(cc=0.3981)	info on Rv2497c/bkdA
Rv0342/iniA	(cc=0.3911)	info on Rv0342/iniA

Correlation of Rv3576/lppH with Rv0140/-

Normalized LFCs for Rv3576/lppH:
(description and provenance of datasets)

	Rv3576/lppH	Rv0140/-
Fe_supp_jason_reseq	-0.753	-0.043
low_pH_jason_reseq	0.35	0.258
NO_jason_reseq	0.029	0.095
B6_jason_reseq	-0.579	0.473
MHCII_jason_reseq	0.829	0.738
Isoniazid02	-0.544	-0.511
Rifampicin4	-0.319	-0.108
Ethambutol3	-0.775	-0.254
Meropenem3	-0.581	-0.273
Vancomycin16	-0.342	-0.042
Rv2680_day32	-0.152	-0.291
H37Rv_KO_MarP	-0.037	-0.075
hypoxia_3wks	-0.419	-0.032
hypoxia_6wks	-0.129	-0.017
glycerol	0.149	0.414
cholesterol	0.164	0.68
AJ	0.19	-0.734
Bibs02	-0.23	0.123
Bibs02c	0.682	0.049
BL6	-0.245	-0.376
BL6a	0.354	0.552
BXD01	0.075	0.723
BXD010	-0.137	0.591
BXD011	0.114	2.057
BXD03	0.622	0.804
BXD04	0.101	0.305
BXD05	0.604	0.039
BXD06	0.546	0.126
BXD07	0.316	0.277
BXD08	0.312	0.167
BXD09	0.148	0.22
CAST	0.077	0.382
CCcont	0.309	0.076
DS01	0.0	0.014
DS02	-0.173	-0.621
DS04	-0.703	-0.343
DS0c	0.539	0.515
GP01	0.527	0.668
GP02	-0.43	0.757
GP0c	-0.534	-0.062
NOD	0.254	-0.08
NZO	0.225	0.023
PWK	-0.085	-0.216
H37Rv_KO_CtpC	0.146	0.431
H37Rv_KO_CtpD	-1.868	-0.832
H37Rv_KO_Rv1272	1.39	0.662
H37Rv_KO_SugABC	1.149	0.697
H37Rv_KO_MbtN	0.052	-0.688
Trans05	0.873	0.574
macrophage_unactivated	0.669	-0.407
IL1	0.0	-0.383
Rapamycin	0.061	-0.325
Tcell	-0.065	-0.274
GMCSF	0.053	-0.523
IFNab	0.692	-0.148
IFNg	-0.334	-0.206
IFNg_GMCSF1	-1.131	-0.5
Rv1432_day32	-0.087	-0.064
Rv1565c_day32	-0.802	-0.73
secA2_input	0.357	-0.778
delta_Rv3594	-0.049	-0.054
delta_Rv3717	-1.354	-0.445
delta_Rv3811	-0.654	0.665
delta_Rv0954	-0.478	0.253
PonA1	-0.321	0.339
EccD1_KO	-1.276	-0.559
EspI_KO	-0.739	-0.26
PE35_KO	-0.376	-0.193
PPE68_KO	-0.598	-0.659
glycerol2	0.018	0.562
lignocerate	0.075	0.69
oleate	0.052	0.448
phosphatidylcholine	0.472	0.268
acetate	-0.151	0.216
glucAc	-0.067	0.222
Rv0950ko	0.633	0.184
Rv1096ko	0.142	0.558
Rv3684ko	0.724	0.606
delta_otsA_trehalose	-0.15	0.52