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 Rv3660c/-:

update plot	correlation	link to info on gene
Rv0532/PE_PGRS6	(cc=0.5743)	info on Rv0532/PE_PGRS6
Rv0478/deoC	(cc=0.5656)	info on Rv0478/deoC
Rv3174/-	(cc=0.4979)	info on Rv3174/-
Rv3273/-	(cc=0.4603)	info on Rv3273/-
Rv2333c/stp	(cc=0.4425)	info on Rv2333c/stp
Rv0533c/fabH	(cc=0.4363)	info on Rv0533c/fabH
Rv3172c/-	(cc=0.4285)	info on Rv3172c/-
Rv1765A/-	(cc=0.4195)	info on Rv1765A/-
Rv1579c/-	(cc=0.4125)	info on Rv1579c/-
Rv3173c/-	(cc=0.4091)	info on Rv3173c/-

Correlation of Rv3660c/- with Rv0532/PE_PGRS6

Normalized LFCs for Rv3660c/-:
(description and provenance of datasets)

	Rv3660c/-	Rv0532/PE_PGRS6
Fe_supp_jason_reseq	-1.174	-0.549
low_pH_jason_reseq	-0.39	-0.708
NO_jason_reseq	-1.68	-0.029
B6_jason_reseq	1.384	-0.538
MHCII_jason_reseq	1.631	1.151
Isoniazid02	2.734	3.355
Rifampicin4	0.926	0.988
Ethambutol3	3.112	2.926
Meropenem3	-0.031	0.242
Vancomycin16	0.687	0.926
Rv2680_day32	-0.642	-0.23
H37Rv_KO_MarP	-0.305	0.095
hypoxia_3wks	0.148	-0.163
hypoxia_6wks	0.43	-0.355
glycerol	0.12	0.162
cholesterol	-0.495	0.145
AJ	-1.084	0.165
Bibs02	1.15	0.268
Bibs02c	1.05	0.505
BL6	0.745	-0.013
BL6a	0.707	0.234
BXD01	-0.098	0.0
BXD010	1.04	-0.478
BXD011	-0.182	-0.494
BXD03	0.017	-0.149
BXD04	0.142	0.225
BXD05	0.735	-0.296
BXD06	0.211	-0.028
BXD07	0.128	0.215
BXD08	1.08	0.653
BXD09	1.01	-0.138
CAST	-1.784	0.095
CCcont	1.045	0.076
DS01	0.517	0.19
DS02	0.939	0.578
DS04	-0.943	0.578
DS0c	1.856	1.065
GP01	-0.257	0.362
GP02	0.01	-0.841
GP0c	0.442	-0.041
NOD	-0.693	-0.583
NZO	0.185	0.514
PWK	-1.469	-0.617
H37Rv_KO_CtpC	-0.668	0.352
H37Rv_KO_CtpD	-0.079	-0.654
H37Rv_KO_Rv1272	-0.58	-0.405
H37Rv_KO_SugABC	-1.619	-0.415
H37Rv_KO_MbtN	-0.938	-0.022
Trans05	-0.661	0.041
macrophage_unactivated	-0.328	0.644
IL1	0.059	0.572
Rapamycin	0.267	0.344
Tcell	-0.74	-0.349
GMCSF	0.61	0.356
IFNab	1.046	-0.039
IFNg	0.158	0.484
IFNg_GMCSF1	0.0	0.314
Rv1432_day32	-0.505	0.0
Rv1565c_day32	1.305	-0.422
secA2_input	0.044	-0.474
delta_Rv3594	-0.702	0.47
delta_Rv3717	-1.034	0.301
delta_Rv3811	-0.654	0.076
delta_Rv0954	-0.284	-0.437
PonA1	-1.551	0.036
EccD1_KO	-0.414	-0.296
EspI_KO	-0.234	-0.593
PE35_KO	0.0	-0.233
PPE68_KO	0.189	-0.221
glycerol2	0.052	-0.025
lignocerate	1.073	0.374
oleate	-2.535	-1.087
phosphatidylcholine	0.783	0.531
acetate	2.173	0.607
glucAc	2.153	0.769
Rv0950ko	0.422	0.202
Rv1096ko	0.489	0.235
Rv3684ko	-1.385	0.36
delta_otsA_trehalose	0.19	-0.756