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 Rv2356c/PPE40:

update plot	correlation	link to info on gene
Rv3650/PE33	(cc=0.5562)	info on Rv3650/PE33
Rv3858c/gltD	(cc=0.5221)	info on Rv3858c/gltD
Rv1918c/PPE35	(cc=0.5179)	info on Rv1918c/PPE35
Rv2735c/-	(cc=0.4971)	info on Rv2735c/-
Rv2190c/-	(cc=0.4896)	info on Rv2190c/-
Rv3489/-	(cc=0.4793)	info on Rv3489/-
Rv2067c/-	(cc=0.4614)	info on Rv2067c/-
Rv2678c/hemE	(cc=0.4582)	info on Rv2678c/hemE
Rv1507A/-	(cc=0.4471)	info on Rv1507A/-
Rv3425/PPE57	(cc=0.4463)	info on Rv3425/PPE57

Correlation of Rv2356c/PPE40 with Rv3489/-

Normalized LFCs for Rv2356c/PPE40:
(description and provenance of datasets)

	Rv2356c/PPE40	Rv3489/-
Fe_supp_jason_reseq	0.65	0.415
low_pH_jason_reseq	0.139	0.0
NO_jason_reseq	-0.984	0.0
B6_jason_reseq	-0.202	0.0
MHCII_jason_reseq	0.447	0.0
Isoniazid02	-0.036	-0.551
Rifampicin4	0.701	1.481
Ethambutol3	0.102	0.251
Meropenem3	-0.138	-0.138
Vancomycin16	0.403	1.451
Rv2680_day32	0.677	0.0
H37Rv_KO_MarP	0.102	0.0
hypoxia_3wks	-0.471	0.0
hypoxia_6wks	-0.405	0.0
glycerol	-0.121	0.0
cholesterol	0.105	0.0
AJ	0.257	0.0
Bibs02	0.147	0.0
Bibs02c	0.456	0.0
BL6	0.519	0.0
BL6a	0.587	0.377
BXD01	-0.225	0.0
BXD010	0.189	0.244
BXD011	0.829	0.0
BXD03	0.435	0.0
BXD04	0.67	0.0
BXD05	0.87	0.369
BXD06	0.547	0.0
BXD07	0.111	0.0
BXD08	-0.177	0.0
BXD09	0.316	0.0
CAST	-0.158	0.0
CCcont	0.049	0.633
DS01	-0.431	0.0
DS02	0.274	0.217
DS04	-0.169	0.37
DS0c	0.107	0.413
GP01	-0.034	0.0
GP02	0.378	0.0
GP0c	-0.477	0.0
NOD	-0.905	0.0
NZO	0.016	0.0
PWK	-0.499	0.0
H37Rv_KO_CtpC	0.105	0.162
H37Rv_KO_CtpD	0.384	0.0
H37Rv_KO_Rv1272	0.847	0.0
H37Rv_KO_SugABC	-0.295	0.189
H37Rv_KO_MbtN	0.957	0.103
Trans05	0.635	0.0
macrophage_unactivated	0.546	0.0
IL1	0.0	0.0
Rapamycin	0.117	0.0
Tcell	-0.293	0.0
GMCSF	0.364	0.0
IFNab	-0.429	0.0
IFNg	0.128	0.0
IFNg_GMCSF1	0.676	0.0
Rv1432_day32	0.018	0.0
Rv1565c_day32	-0.504	0.415
secA2_input	-1.141	-1.868
delta_Rv3594	0.626	-0.193
delta_Rv3717	-0.292	-0.331
delta_Rv3811	0.544	0.0
delta_Rv0954	0.686	0.0
PonA1	0.329	-0.304
EccD1_KO	-0.816	-4.285
EspI_KO	-0.836	-2.966
PE35_KO	-0.802	-3.034
PPE68_KO	-0.851	-3.868
glycerol2	-0.153	-2.081
lignocerate	-0.056	-1.808
oleate	-0.109	-2.105
phosphatidylcholine	-0.343	-2.08
acetate	0.595	-0.472
glucAc	0.061	-1.535
Rv0950ko	-0.139	-0.621
Rv1096ko	-0.561	0.0
Rv3684ko	-0.524	0.305
delta_otsA_trehalose	0.269	-1.193