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 Rv2495c/bkdC

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

	Rv3070/-	Rv2495c/bkdC
Fe_supp_jason_reseq	-0.529	-5.05
low_pH_jason_reseq	-0.878	-5.352
NO_jason_reseq	-0.494	0.252
B6_jason_reseq	-1.15	-2.921
MHCII_jason_reseq	-0.669	-2.608
Isoniazid02	-0.035	0.333
Rifampicin4	-0.996	-1.652
Ethambutol3	-0.524	-0.332
Meropenem3	-0.422	-0.061
Vancomycin16	-0.369	0.0
Rv2680_day32	0.899	-0.168
H37Rv_KO_MarP	0.233	0.769
hypoxia_3wks	-0.088	0.263
hypoxia_6wks	0.28	0.069
glycerol	-0.788	-0.628
cholesterol	-0.981	0.684
AJ	1.077	-0.914
Bibs02	0.838	-1.495
Bibs02c	1.085	0.735
BL6	0.327	-0.869
BL6a	1.378	0.973
BXD01	0.993	0.0
BXD010	0.792	-0.622
BXD011	0.285	0.448
BXD03	1.018	1.318
BXD04	0.43	0.78
BXD05	0.237	0.078
BXD06	1.196	0.441
BXD07	0.75	-0.375
BXD08	0.944	0.702
BXD09	0.991	0.232
CAST	0.586	-0.537
CCcont	1.06	-0.797
DS01	-0.068	0.204
DS02	0.469	0.52
DS04	1.018	1.159
DS0c	0.273	1.538
GP01	-0.706	0.085
GP02	-1.474	-0.797
GP0c	-0.117	-0.903
NOD	1.015	-0.986
NZO	-0.724	-0.186
PWK	0.735	0.222
H37Rv_KO_CtpC	0.934	0.5
H37Rv_KO_CtpD	0.44	0.333
H37Rv_KO_Rv1272	0.637	0.434
H37Rv_KO_SugABC	-1.705	-0.877
H37Rv_KO_MbtN	-1.164	-0.32
Trans05	0.445	1.474
macrophage_unactivated	0.726	0.994
IL1	0.771	1.258
Rapamycin	0.393	0.697
Tcell	0.626	0.74
GMCSF	0.317	-0.19
IFNab	0.212	-0.109
IFNg	0.831	0.358
IFNg_GMCSF1	1.241	0.217
Rv1432_day32	-0.257	0.0
Rv1565c_day32	0.12	-0.395
secA2_input	-0.177	-0.611
delta_Rv3594	1.054	-0.561
delta_Rv3717	-1.258	-0.076
delta_Rv3811	0.043	-0.546
delta_Rv0954	0.89	-0.078
PonA1	0.177	-0.874
EccD1_KO	-0.082	-0.898
EspI_KO	-0.736	-1.962
PE35_KO	1.138	-0.709
PPE68_KO	0.08	-0.246
glycerol2	0.342	-0.68
lignocerate	0.485	-0.591
oleate	0.116	0.142
phosphatidylcholine	0.312	-0.398
acetate	0.146	-1.197
glucAc	0.102	-1.535
Rv0950ko	0.709	0.754
Rv1096ko	1.173	1.221
Rv3684ko	2.227	1.608
delta_otsA_trehalose	0.049	-1.661