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 Rv1662/pks8

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

	Rv3070/-	Rv1662/pks8
Fe_supp_jason_reseq	-0.529	-0.458
low_pH_jason_reseq	-0.878	0.403
NO_jason_reseq	-0.494	-0.362
B6_jason_reseq	-1.15	-0.97
MHCII_jason_reseq	-0.669	-0.509
Isoniazid02	-0.035	-0.767
Rifampicin4	-0.996	-1.097
Ethambutol3	-0.524	-0.313
Meropenem3	-0.422	-1.234
Vancomycin16	-0.369	-0.974
Rv2680_day32	0.899	-0.228
H37Rv_KO_MarP	0.233	-0.214
hypoxia_3wks	-0.088	0.55
hypoxia_6wks	0.28	0.378
glycerol	-0.788	-0.471
cholesterol	-0.981	-0.583
AJ	1.077	0.274
Bibs02	0.838	0.531
Bibs02c	1.085	-0.279
BL6	0.327	0.739
BL6a	1.378	0.637
BXD01	0.993	0.496
BXD010	0.792	0.873
BXD011	0.285	0.626
BXD03	1.018	0.699
BXD04	0.43	0.64
BXD05	0.237	0.513
BXD06	1.196	0.69
BXD07	0.75	0.75
BXD08	0.944	0.786
BXD09	0.991	0.615
CAST	0.586	0.095
CCcont	1.06	0.694
DS01	-0.068	-0.205
DS02	0.469	-0.397
DS04	1.018	0.436
DS0c	0.273	-0.189
GP01	-0.706	0.584
GP02	-1.474	-0.111
GP0c	-0.117	0.154
NOD	1.015	0.0
NZO	-0.724	-0.364
PWK	0.735	0.44
H37Rv_KO_CtpC	0.934	1.072
H37Rv_KO_CtpD	0.44	0.368
H37Rv_KO_Rv1272	0.637	1.677
H37Rv_KO_SugABC	-1.705	-0.601
H37Rv_KO_MbtN	-1.164	1.817
Trans05	0.445	0.891
macrophage_unactivated	0.726	1.016
IL1	0.771	0.558
Rapamycin	0.393	0.353
Tcell	0.626	0.375
GMCSF	0.317	-0.108
IFNab	0.212	0.348
IFNg	0.831	0.775
IFNg_GMCSF1	1.241	0.911
Rv1432_day32	-0.257	0.143
Rv1565c_day32	0.12	0.212
secA2_input	-0.177	-0.197
delta_Rv3594	1.054	0.474
delta_Rv3717	-1.258	0.269
delta_Rv3811	0.043	0.461
delta_Rv0954	0.89	0.46
PonA1	0.177	-0.966
EccD1_KO	-0.082	-0.151
EspI_KO	-0.736	-0.405
PE35_KO	1.138	0.831
PPE68_KO	0.08	0.793
glycerol2	0.342	-0.531
lignocerate	0.485	-0.093
oleate	0.116	-0.469
phosphatidylcholine	0.312	-0.106
acetate	0.146	-0.062
glucAc	0.102	0.146
Rv0950ko	0.709	0.13
Rv1096ko	1.173	1.05
Rv3684ko	2.227	0.789
delta_otsA_trehalose	0.049	-0.15