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 Rv0489/gpm1

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

	Rv3208/-	Rv0489/gpm1
Fe_supp_jason_reseq	4.191	5.175
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	0.0
Rifampicin4	0.0	0.0
Ethambutol3	0.0	0.0
Meropenem3	0.0	0.0
Vancomycin16	0.0	0.0
Rv2680_day32	0.0	0.0
H37Rv_KO_MarP	-1.705	-3.277
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	0.0
BXD01	0.0	0.0
BXD010	0.352	0.0
BXD011	0.35	0.626
BXD03	0.0	0.0
BXD04	0.0	0.0
BXD05	0.135	0.0
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	2.416
DS01	0.0	0.0
DS02	0.0	0.0
DS04	0.682	0.37
DS0c	0.0	0.0
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	0.241
H37Rv_KO_Rv1272	0.141	0.0
H37Rv_KO_SugABC	0.348	0.272
H37Rv_KO_MbtN	0.196	0.437
Trans05	0.131	0.131
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	0.0
secA2_input	-1.368	-1.628
delta_Rv3594	1.487	-0.113
delta_Rv3717	1.223	-0.781
delta_Rv3811	-0.171	-0.617
delta_Rv0954	-0.149	2.74
PonA1	-0.204	-1.154
EccD1_KO	-1.204	-0.141
EspI_KO	0.0	0.456
PE35_KO	-2.981	-0.061
PPE68_KO	-2.742	-0.352
glycerol2	-0.82	-0.531
lignocerate	-0.712	-0.462
oleate	-0.829	-0.537
phosphatidylcholine	-0.819	-0.531
acetate	-0.973	-0.63
glucAc	-0.605	-0.392
Rv0950ko	0.311	-0.172
Rv1096ko	-0.513	-2.799
Rv3684ko	0.17	-1.651
delta_otsA_trehalose	0.0	-0.468