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 Rv3208/-:

update plot	correlation	link to info on gene
Rv0955/-	(cc=0.6447)	info on Rv0955/-
Rv0637/hadC	(cc=0.6115)	info on Rv0637/hadC
Rv0489/gpm1	(cc=0.6022)	info on Rv0489/gpm1
Rv3489/-	(cc=0.5782)	info on Rv3489/-
Rv2221c/glnE	(cc=0.5758)	info on Rv2221c/glnE
Rv2678c/hemE	(cc=0.5631)	info on Rv2678c/hemE
Rv3918c/parA	(cc=0.5424)	info on Rv3918c/parA
Rv3753c/-	(cc=0.5422)	info on Rv3753c/-
Rv1565c/-	(cc=0.5311)	info on Rv1565c/-
Rv2553c/-	(cc=0.5213)	info on Rv2553c/-

Correlation of Rv3208/- with Rv3489/-

Normalized LFCs for Rv3208/-:
(description and provenance of datasets)

	Rv3208/-	Rv3489/-
Fe_supp_jason_reseq	4.191	0.415
low_pH_jason_reseq	0.0	0.0
NO_jason_reseq	0.0	0.0
B6_jason_reseq	0.0	0.0
MHCII_jason_reseq	0.0	0.0
Isoniazid02	0.0	-0.551
Rifampicin4	0.0	1.481
Ethambutol3	0.0	0.251
Meropenem3	0.0	-0.138
Vancomycin16	0.0	1.451
Rv2680_day32	0.0	0.0
H37Rv_KO_MarP	-1.705	0.0
hypoxia_3wks	-0.55	0.0
hypoxia_6wks	-0.288	0.0
glycerol	0.0	0.0
cholesterol	0.0	0.0
AJ	0.0	0.0
Bibs02	0.0	0.0
Bibs02c	0.0	0.0
BL6	0.768	0.0
BL6a	0.0	0.377
BXD01	0.0	0.0
BXD010	0.352	0.244
BXD011	0.35	0.0
BXD03	0.0	0.0
BXD04	0.0	0.0
BXD05	0.135	0.369
BXD06	0.0	0.0
BXD07	0.0	0.0
BXD08	0.0	0.0
BXD09	0.0	0.0
CAST	0.0	0.0
CCcont	1.43	0.633
DS01	0.0	0.0
DS02	0.0	0.217
DS04	0.682	0.37
DS0c	0.0	0.413
GP01	0.0	0.0
GP02	0.0	0.0
GP0c	0.357	0.0
NOD	0.0	0.0
NZO	0.0	0.0
PWK	0.0	0.0
H37Rv_KO_CtpC	0.0	0.162
H37Rv_KO_CtpD	0.0	0.0
H37Rv_KO_Rv1272	0.141	0.0
H37Rv_KO_SugABC	0.348	0.189
H37Rv_KO_MbtN	0.196	0.103
Trans05	0.131	0.0
macrophage_unactivated	0.398	0.0
IL1	0.374	0.0
Rapamycin	1.068	0.0
Tcell	0.0	0.0
GMCSF	0.333	0.0
IFNab	0.729	0.0
IFNg	0.93	0.0
IFNg_GMCSF1	0.396	0.0
Rv1432_day32	0.0	0.0
Rv1565c_day32	0.0	0.415
secA2_input	-1.368	-1.868
delta_Rv3594	1.487	-0.193
delta_Rv3717	1.223	-0.331
delta_Rv3811	-0.171	0.0
delta_Rv0954	-0.149	0.0
PonA1	-0.204	-0.304
EccD1_KO	-1.204	-4.285
EspI_KO	0.0	-2.966
PE35_KO	-2.981	-3.034
PPE68_KO	-2.742	-3.868
glycerol2	-0.82	-2.081
lignocerate	-0.712	-1.808
oleate	-0.829	-2.105
phosphatidylcholine	-0.819	-2.08
acetate	-0.973	-0.472
glucAc	-0.605	-1.535
Rv0950ko	0.311	-0.621
Rv1096ko	-0.513	0.0
Rv3684ko	0.17	0.305
delta_otsA_trehalose	0.0	-1.193