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 Rv0654/-:

update plot	correlation	link to info on gene
Rv2590/fadD9	(cc=0.6053)	info on Rv2590/fadD9
Rv2495c/bkdC	(cc=0.5864)	info on Rv2495c/bkdC
Rv2770c/PPE44	(cc=0.5132)	info on Rv2770c/PPE44
Rv1844c/gnd1	(cc=0.5072)	info on Rv1844c/gnd1
Rv3440c/-	(cc=0.4989)	info on Rv3440c/-
Rv3558/PPE64	(cc=0.4858)	info on Rv3558/PPE64
Rv0222/echA1	(cc=0.4802)	info on Rv0222/echA1
Rv0826/-	(cc=0.4795)	info on Rv0826/-
Rv0281/-	(cc=0.4727)	info on Rv0281/-
Rv2579/dhaA	(cc=0.4699)	info on Rv2579/dhaA

Correlation of Rv0654/- with Rv3440c/-

Normalized LFCs for Rv0654/-:
(description and provenance of datasets)

	Rv0654/-	Rv3440c/-
Fe_supp_jason_reseq	-1.487	-0.278
low_pH_jason_reseq	-2.16	-0.925
NO_jason_reseq	0.706	-0.788
B6_jason_reseq	-0.841	-0.178
MHCII_jason_reseq	-0.807	-0.112
Isoniazid02	0.458	0.838
Rifampicin4	-0.263	0.85
Ethambutol3	1.187	0.817
Meropenem3	0.234	0.724
Vancomycin16	-0.308	0.517
Rv2680_day32	0.07	0.505
H37Rv_KO_MarP	0.114	-0.023
hypoxia_3wks	-0.144	0.152
hypoxia_6wks	0.169	0.0
glycerol	-0.361	0.758
cholesterol	-0.111	0.088
AJ	0.435	0.615
Bibs02	0.122	0.668
Bibs02c	0.426	0.299
BL6	0.212	-0.197
BL6a	-0.095	0.113
BXD01	0.139	0.243
BXD010	-0.658	-0.789
BXD011	0.296	-1.159
BXD03	-0.278	-0.563
BXD04	0.053	0.079
BXD05	-0.428	-0.97
BXD06	-0.155	-0.476
BXD07	-0.152	-0.377
BXD08	0.054	0.037
BXD09	-0.216	0.019
CAST	0.309	0.417
CCcont	-0.22	-0.107
DS01	0.327	0.874
DS02	0.249	0.837
DS04	0.627	0.86
DS0c	0.547	0.701
GP01	0.208	0.0
GP02	0.613	1.055
GP0c	0.129	0.213
NOD	0.693	0.181
NZO	0.081	0.811
PWK	0.08	0.244
H37Rv_KO_CtpC	-0.213	0.537
H37Rv_KO_CtpD	0.051	0.796
H37Rv_KO_Rv1272	0.049	0.343
H37Rv_KO_SugABC	0.384	1.312
H37Rv_KO_MbtN	0.231	0.29
Trans05	-0.465	0.018
macrophage_unactivated	0.391	-0.464
IL1	0.297	-0.065
Rapamycin	0.319	0.178
Tcell	-0.456	-0.42
GMCSF	0.684	-0.293
IFNab	-0.027	0.417
IFNg	0.425	0.222
IFNg_GMCSF1	0.277	0.101
Rv1432_day32	0.489	0.158
Rv1565c_day32	-0.024	-0.316
secA2_input	0.352	-0.124
delta_Rv3594	-0.148	-0.285
delta_Rv3717	-0.277	-0.643
delta_Rv3811	-0.058	-0.223
delta_Rv0954	0.318	-0.398
PonA1	-0.373	-0.63
EccD1_KO	0.151	-0.237
EspI_KO	-0.183	-0.011
PE35_KO	-0.694	-0.061
PPE68_KO	-0.761	-0.147
glycerol2	0.773	1.042
lignocerate	0.561	0.56
oleate	0.851	1.059
phosphatidylcholine	0.664	0.737
acetate	-0.351	0.17
glucAc	-0.288	-0.134
Rv0950ko	0.627	0.805
Rv1096ko	0.715	0.434
Rv3684ko	0.413	0.694
delta_otsA_trehalose	-0.301	-0.583