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 Rv2259/mscR:

update plot	correlation	link to info on gene
Rv1908c/katG	(cc=0.6783)	info on Rv1908c/katG
Rv2221c/glnE	(cc=0.6365)	info on Rv2221c/glnE
Rv3261/fbiA	(cc=0.5918)	info on Rv3261/fbiA
Rv2737c/recA	(cc=0.5914)	info on Rv2737c/recA
Rv1170/mshB	(cc=0.5855)	info on Rv1170/mshB
Rv0003/recF	(cc=0.5795)	info on Rv0003/recF
Rv1701/-	(cc=0.5675)	info on Rv1701/-
Rv1633/uvrB	(cc=0.5572)	info on Rv1633/uvrB
Rv3715c/recR	(cc=0.5395)	info on Rv3715c/recR
Rv0489/gpm1	(cc=0.5289)	info on Rv0489/gpm1

Correlation of Rv2259/mscR with Rv1908c/katG

Normalized LFCs for Rv2259/mscR:
(description and provenance of datasets)

	Rv2259/mscR	Rv1908c/katG
Fe_supp_jason_reseq	3.863	2.303
low_pH_jason_reseq	0.211	-0.44
NO_jason_reseq	0.0	-0.69
B6_jason_reseq	-0.153	-0.292
MHCII_jason_reseq	-0.135	-0.257
Isoniazid02	-1.385	0.0
Rifampicin4	0.774	0.0
Ethambutol3	-0.991	0.0
Meropenem3	-2.803	0.0
Vancomycin16	-0.65	0.0
Rv2680_day32	0.0	0.0
H37Rv_KO_MarP	-0.416	-1.722
hypoxia_3wks	-1.543	-0.977
hypoxia_6wks	-0.585	-2.714
glycerol	0.992	0.0
cholesterol	1.194	0.0
AJ	0.815	0.0
Bibs02	0.0	0.0
Bibs02c	0.0	0.0
BL6	0.343	0.238
BL6a	0.198	0.544
BXD01	0.13	0.248
BXD010	0.0	0.0
BXD011	0.243	0.854
BXD03	0.258	0.0
BXD04	0.607	0.34
BXD05	0.135	0.661
BXD06	0.656	0.469
BXD07	0.0	0.0
BXD08	0.0	0.365
BXD09	0.386	0.69
CAST	0.0	0.0
CCcont	3.429	3.165
DS01	0.236	0.0
DS02	0.0	0.0
DS04	0.822	0.953
DS0c	0.0	0.0
GP01	0.271	0.0
GP02	0.0	0.0
GP0c	0.248	0.0
NOD	0.0	0.0
NZO	0.199	0.0
PWK	0.374	0.0
H37Rv_KO_CtpC	0.162	0.446
H37Rv_KO_CtpD	0.537	0.703
H37Rv_KO_Rv1272	0.141	0.141
H37Rv_KO_SugABC	0.487	0.42
H37Rv_KO_MbtN	0.691	2.414
Trans05	0.0	0.359
macrophage_unactivated	0.436	0.0
IL1	0.0	0.0
Rapamycin	0.0	0.0
Tcell	0.0	0.0
GMCSF	0.0	0.0
IFNab	0.0	0.417
IFNg	0.0	0.0
IFNg_GMCSF1	0.0	0.0
Rv1432_day32	0.0	-0.494
Rv1565c_day32	0.0	0.0
secA2_input	-2.259	0.67
delta_Rv3594	-0.493	0.907
delta_Rv3717	-1.023	0.784
delta_Rv3811	0.336	0.812
delta_Rv0954	0.912	0.842
PonA1	-0.851	-0.419
EccD1_KO	-1.704	-4.969
EspI_KO	-3.434	-4.743
PE35_KO	1.625	1.374
PPE68_KO	-0.269	0.275
glycerol2	-0.745	-3.698
lignocerate	-0.812	-2.548
oleate	-2.101	-3.077
phosphatidylcholine	-1.877	-3.546
acetate	0.226	0.253
glucAc	0.269	-0.375
Rv0950ko	-0.211	-1.212
Rv1096ko	-0.434	-1.493
Rv3684ko	0.429	-0.298
delta_otsA_trehalose	0.164	0.153