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 Rv3070/-:

update plot	correlation	link to info on gene
Rv1662/pks8	(cc=0.5061)	info on Rv1662/pks8
Rv1419/-	(cc=0.4987)	info on Rv1419/-
Rv0276/-	(cc=0.4657)	info on Rv0276/-
Rv2495c/bkdC	(cc=0.4624)	info on Rv2495c/bkdC
Rv0827c/kmtR	(cc=0.4484)	info on Rv0827c/kmtR
Rv3140/fadE23	(cc=0.4449)	info on Rv3140/fadE23
Rv2211c/gcvT	(cc=0.4339)	info on Rv2211c/gcvT
Rv3626c/-	(cc=0.4311)	info on Rv3626c/-
Rv2833c/ugpB	(cc=0.4288)	info on Rv2833c/ugpB
Rv2767c/-	(cc=0.4193)	info on Rv2767c/-

Correlation of Rv3070/- with Rv0827c/kmtR

Normalized LFCs for Rv3070/-:
(description and provenance of datasets)

	Rv3070/-	Rv0827c/kmtR
Fe_supp_jason_reseq	-0.529	-2.06
low_pH_jason_reseq	-0.878	1.128
NO_jason_reseq	-0.494	-0.942
B6_jason_reseq	-1.15	-2.511
MHCII_jason_reseq	-0.669	-3.0
Isoniazid02	-0.035	-1.307
Rifampicin4	-0.996	0.303
Ethambutol3	-0.524	-0.845
Meropenem3	-0.422	-1.276
Vancomycin16	-0.369	-0.883
Rv2680_day32	0.899	0.018
H37Rv_KO_MarP	0.233	1.192
hypoxia_3wks	-0.088	-0.694
hypoxia_6wks	0.28	0.416
glycerol	-0.788	-1.401
cholesterol	-0.981	-0.766
AJ	1.077	0.301
Bibs02	0.838	0.954
Bibs02c	1.085	-0.629
BL6	0.327	0.837
BL6a	1.378	0.387
BXD01	0.993	0.703
BXD010	0.792	0.131
BXD011	0.285	1.34
BXD03	1.018	-0.25
BXD04	0.43	0.562
BXD05	0.237	0.499
BXD06	1.196	0.849
BXD07	0.75	0.96
BXD08	0.944	0.656
BXD09	0.991	1.112
CAST	0.586	0.48
CCcont	1.06	1.683
DS01	-0.068	-1.372
DS02	0.469	0.9
DS04	1.018	0.304
DS0c	0.273	0.368
GP01	-0.706	-1.978
GP02	-1.474	-1.667
GP0c	-0.117	-2.605
NOD	1.015	0.068
NZO	-0.724	0.63
PWK	0.735	0.145
H37Rv_KO_CtpC	0.934	3.761
H37Rv_KO_CtpD	0.44	1.266
H37Rv_KO_Rv1272	0.637	1.942
H37Rv_KO_SugABC	-1.705	-0.63
H37Rv_KO_MbtN	-1.164	-0.289
Trans05	0.445	1.185
macrophage_unactivated	0.726	1.288
IL1	0.771	-0.581
Rapamycin	0.393	0.347
Tcell	0.626	1.58
GMCSF	0.317	0.333
IFNab	0.212	1.176
IFNg	0.831	1.539
IFNg_GMCSF1	1.241	-0.962
Rv1432_day32	-0.257	-0.763
Rv1565c_day32	0.12	-0.134
secA2_input	-0.177	0.244
delta_Rv3594	1.054	-0.85
delta_Rv3717	-1.258	-1.097
delta_Rv3811	0.043	-0.233
delta_Rv0954	0.89	1.264
PonA1	0.177	1.221
EccD1_KO	-0.082	0.99
EspI_KO	-0.736	1.526
PE35_KO	1.138	0.12
PPE68_KO	0.08	0.739
glycerol2	0.342	-1.473
lignocerate	0.485	-0.48
oleate	0.116	-1.859
phosphatidylcholine	0.312	-0.866
acetate	0.146	-0.048
glucAc	0.102	0.626
Rv0950ko	0.709	0.669
Rv1096ko	1.173	-0.106
Rv3684ko	2.227	0.681
delta_otsA_trehalose	0.049	1.027