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 Rv1908c/katG:

update plot	correlation	link to info on gene
Rv2259/mscR	(cc=0.6783)	info on Rv2259/mscR
Rv3715c/recR	(cc=0.6779)	info on Rv3715c/recR
Rv1420/uvrC	(cc=0.6662)	info on Rv1420/uvrC
Rv1633/uvrB	(cc=0.663)	info on Rv1633/uvrB
Rv1173/fbiC	(cc=0.628)	info on Rv1173/fbiC
Rv1701/-	(cc=0.618)	info on Rv1701/-
Rv2198c/mmpS3	(cc=0.6134)	info on Rv2198c/mmpS3
Rv1638/uvrA	(cc=0.6103)	info on Rv1638/uvrA
Rv2373c/dnaJ2	(cc=0.5982)	info on Rv2373c/dnaJ2
Rv3624c/hpt	(cc=0.5969)	info on Rv3624c/hpt

Correlation of Rv1908c/katG with Rv3715c/recR

Normalized LFCs for Rv1908c/katG:
(description and provenance of datasets)

	Rv1908c/katG	Rv3715c/recR
Fe_supp_jason_reseq	2.303	2.883
low_pH_jason_reseq	-0.44	0.0
NO_jason_reseq	-0.69	-1.993
B6_jason_reseq	-0.292	-0.413
MHCII_jason_reseq	-0.257	-0.283
Isoniazid02	0.0	0.987
Rifampicin4	0.0	-0.357
Ethambutol3	0.0	0.574
Meropenem3	0.0	0.223
Vancomycin16	0.0	-0.976
Rv2680_day32	0.0	-0.642
H37Rv_KO_MarP	-1.722	-1.411
hypoxia_3wks	-0.977	-0.522
hypoxia_6wks	-2.714	-0.576
glycerol	0.0	1.537
cholesterol	0.0	0.463
AJ	0.0	0.324
Bibs02	0.0	0.371
Bibs02c	0.0	-0.527
BL6	0.238	0.649
BL6a	0.544	0.0
BXD01	0.248	0.79
BXD010	0.0	0.722
BXD011	0.854	0.0
BXD03	0.0	1.448
BXD04	0.34	0.395
BXD05	0.661	0.502
BXD06	0.469	0.566
BXD07	0.0	1.445
BXD08	0.365	1.351
BXD09	0.69	0.285
CAST	0.0	-0.809
CCcont	3.165	2.556
DS01	0.0	0.171
DS02	0.0	-0.764
DS04	0.953	0.394
DS0c	0.0	0.157
GP01	0.0	1.484
GP02	0.0	0.06
GP0c	0.0	0.893
NOD	0.0	-0.566
NZO	0.0	1.124
PWK	0.0	-0.494
H37Rv_KO_CtpC	0.446	2.019
H37Rv_KO_CtpD	0.703	0.537
H37Rv_KO_Rv1272	0.141	-0.495
H37Rv_KO_SugABC	0.42	1.605
H37Rv_KO_MbtN	2.414	0.487
Trans05	0.359	0.344
macrophage_unactivated	0.0	0.669
IL1	0.0	-1.011
Rapamycin	0.0	-0.491
Tcell	0.0	1.098
GMCSF	0.0	-1.444
IFNab	0.417	-0.236
IFNg	0.0	-0.911
IFNg_GMCSF1	0.0	-0.779
Rv1432_day32	-0.494	0.0
Rv1565c_day32	0.0	-0.766
secA2_input	0.67	0.994
delta_Rv3594	0.907	0.961
delta_Rv3717	0.784	0.257
delta_Rv3811	0.812	0.934
delta_Rv0954	0.842	1.145
PonA1	-0.419	0.145
EccD1_KO	-4.969	-1.786
EspI_KO	-4.743	-2.772
PE35_KO	1.374	-0.817
PPE68_KO	0.275	-1.805
glycerol2	-3.698	-2.434
lignocerate	-2.548	-2.02
oleate	-3.077	-1.961
phosphatidylcholine	-3.546	-2.027
acetate	0.253	-0.166
glucAc	-0.375	0.605
Rv0950ko	-1.212	-0.926
Rv1096ko	-1.493	0.507
Rv3684ko	-0.298	1.094
delta_otsA_trehalose	0.153	0.83