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 Rv0122/-:

update plot	correlation	link to info on gene
Rv3218/-	(cc=0.6128)	info on Rv3218/-
Rv3847/-	(cc=0.5734)	info on Rv3847/-
Rv0928/pstS3	(cc=0.5712)	info on Rv0928/pstS3
Rv1239c/corA	(cc=0.5701)	info on Rv1239c/corA
Rv1278/-	(cc=0.5447)	info on Rv1278/-
Rv0930/pstA1	(cc=0.5421)	info on Rv0930/pstA1
Rv2243/fabD	(cc=0.5392)	info on Rv2243/fabD
Rv0048c/-	(cc=0.5365)	info on Rv0048c/-
Rv0820/phoT	(cc=0.532)	info on Rv0820/phoT
Rv0371c/-	(cc=0.5288)	info on Rv0371c/-

Correlation of Rv0122/- with Rv3218/-

Normalized LFCs for Rv0122/-:
(description and provenance of datasets)

	Rv0122/-	Rv3218/-
Fe_supp_jason_reseq	-0.895	0.069
low_pH_jason_reseq	0.465	0.626
NO_jason_reseq	-0.144	-0.039
B6_jason_reseq	-1.234	0.103
MHCII_jason_reseq	-0.503	-0.977
Isoniazid02	-0.138	-0.997
Rifampicin4	-0.533	-0.479
Ethambutol3	0.323	-0.966
Meropenem3	0.319	-0.543
Vancomycin16	-0.125	-1.167
Rv2680_day32	-0.249	0.234
H37Rv_KO_MarP	1.28	0.319
hypoxia_3wks	0.435	0.502
hypoxia_6wks	1.823	0.833
glycerol	0.936	-0.357
cholesterol	0.759	0.85
AJ	1.284	-0.338
Bibs02	-0.091	0.211
Bibs02c	0.577	0.317
BL6	1.781	1.984
BL6a	1.26	1.934
BXD01	1.547	2.36
BXD010	2.444	2.075
BXD011	0.741	2.479
BXD03	1.926	1.262
BXD04	0.736	2.489
BXD05	1.72	2.15
BXD06	1.647	2.326
BXD07	2.188	2.605
BXD08	1.427	1.872
BXD09	1.984	2.198
CAST	1.241	-0.299
CCcont	1.007	0.557
DS01	0.823	-0.2
DS02	1.074	0.225
DS04	-1.099	0.51
DS0c	-0.108	0.303
GP01	2.709	1.142
GP02	1.354	1.904
GP0c	1.67	1.108
NOD	-0.552	-0.586
NZO	2.274	1.334
PWK	1.491	1.225
H37Rv_KO_CtpC	0.945	0.148
H37Rv_KO_CtpD	0.854	1.334
H37Rv_KO_Rv1272	-0.144	1.52
H37Rv_KO_SugABC	0.292	1.485
H37Rv_KO_MbtN	2.117	2.303
Trans05	-0.915	1.743
macrophage_unactivated	-0.136	-0.628
IL1	-0.062	0.561
Rapamycin	-1.145	0.822
Tcell	0.068	0.075
GMCSF	0.523	0.906
IFNab	-0.438	0.045
IFNg	-1.147	0.43
IFNg_GMCSF1	0.195	-0.487
Rv1432_day32	-0.256	0.963
Rv1565c_day32	0.085	-0.682
secA2_input	1.088	0.848
delta_Rv3594	-0.182	-0.846
delta_Rv3717	-0.917	0.467
delta_Rv3811	-0.77	-0.464
delta_Rv0954	-0.547	-0.783
PonA1	-1.128	-0.658
EccD1_KO	-0.944	-0.516
EspI_KO	-1.252	-1.144
PE35_KO	-0.07	-0.487
PPE68_KO	-0.477	-1.245
glycerol2	-1.286	-0.859
lignocerate	-0.564	-1.679
oleate	0.465	-1.16
phosphatidylcholine	-0.91	-1.931
acetate	-0.327	-0.6
glucAc	-1.472	-0.508
Rv0950ko	0.953	0.286
Rv1096ko	1.463	0.0
Rv3684ko	2.659	0.743
delta_otsA_trehalose	0.667	2.083