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 Rv2259/mscR

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

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