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 Rv3626c/-

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

	Rv3070/-	Rv3626c/-
Fe_supp_jason_reseq	-0.529	0.434
low_pH_jason_reseq	-0.878	-1.315
NO_jason_reseq	-0.494	-0.622
B6_jason_reseq	-1.15	-0.85
MHCII_jason_reseq	-0.669	0.317
Isoniazid02	-0.035	-0.383
Rifampicin4	-0.996	-0.533
Ethambutol3	-0.524	0.426
Meropenem3	-0.422	-0.295
Vancomycin16	-0.369	-0.353
Rv2680_day32	0.899	1.185
H37Rv_KO_MarP	0.233	0.241
hypoxia_3wks	-0.088	-0.566
hypoxia_6wks	0.28	-0.39
glycerol	-0.788	-0.047
cholesterol	-0.981	0.142
AJ	1.077	0.128
Bibs02	0.838	0.359
Bibs02c	1.085	0.226
BL6	0.327	0.314
BL6a	1.378	0.462
BXD01	0.993	0.072
BXD010	0.792	0.431
BXD011	0.285	1.433
BXD03	1.018	0.265
BXD04	0.43	1.156
BXD05	0.237	0.486
BXD06	1.196	-0.195
BXD07	0.75	0.285
BXD08	0.944	0.381
BXD09	0.991	0.289
CAST	0.586	0.319
CCcont	1.06	0.949
DS01	-0.068	1.206
DS02	0.469	1.018
DS04	1.018	1.134
DS0c	0.273	0.767
GP01	-0.706	-0.589
GP02	-1.474	-0.329
GP0c	-0.117	-0.472
NOD	1.015	-0.329
NZO	-0.724	-0.069
PWK	0.735	-0.186
H37Rv_KO_CtpC	0.934	0.493
H37Rv_KO_CtpD	0.44	1.061
H37Rv_KO_Rv1272	0.637	-1.054
H37Rv_KO_SugABC	-1.705	-0.392
H37Rv_KO_MbtN	-1.164	-0.635
Trans05	0.445	-0.141
macrophage_unactivated	0.726	0.47
IL1	0.771	-0.323
Rapamycin	0.393	-0.08
Tcell	0.626	-0.45
GMCSF	0.317	0.723
IFNab	0.212	0.762
IFNg	0.831	0.615
IFNg_GMCSF1	1.241	-0.255
Rv1432_day32	-0.257	-1.228
Rv1565c_day32	0.12	0.223
secA2_input	-0.177	-0.676
delta_Rv3594	1.054	-0.185
delta_Rv3717	-1.258	-0.586
delta_Rv3811	0.043	0.299
delta_Rv0954	0.89	0.296
PonA1	0.177	1.095
EccD1_KO	-0.082	0.822
EspI_KO	-0.736	0.684
PE35_KO	1.138	0.729
PPE68_KO	0.08	0.918
glycerol2	0.342	0.905
lignocerate	0.485	0.826
oleate	0.116	-0.818
phosphatidylcholine	0.312	0.427
acetate	0.146	1.456
glucAc	0.102	1.246
Rv0950ko	0.709	1.505
Rv1096ko	1.173	1.538
Rv3684ko	2.227	1.634
delta_otsA_trehalose	0.049	-0.151