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 Rv1317c/alkA:

update plot	correlation	link to info on gene
Rv1368/lprF	(cc=0.4752)	info on Rv1368/lprF
Rv2394/ggtB	(cc=0.471)	info on Rv2394/ggtB
Rv1290c/-	(cc=0.4682)	info on Rv1290c/-
Rv2484c/-	(cc=0.4676)	info on Rv2484c/-
Rv2715/-	(cc=0.4611)	info on Rv2715/-
Rv2701c/suhB	(cc=0.4335)	info on Rv2701c/suhB
Rv0338c/-	(cc=0.4296)	info on Rv0338c/-
Rv0069c/sdaA	(cc=0.4268)	info on Rv0069c/sdaA
Rv2189c/-	(cc=0.4138)	info on Rv2189c/-
Rv0484c/-	(cc=0.4084)	info on Rv0484c/-

Correlation of Rv1317c/alkA with Rv0338c/-

Normalized LFCs for Rv1317c/alkA:
(description and provenance of datasets)

	Rv1317c/alkA	Rv0338c/-
Fe_supp_jason_reseq	-0.628	0.0
low_pH_jason_reseq	-1.337	0.0
NO_jason_reseq	-0.711	0.0
B6_jason_reseq	-0.498	0.0
MHCII_jason_reseq	-0.365	0.0
Isoniazid02	1.264	0.0
Rifampicin4	0.062	0.0
Ethambutol3	1.267	0.0
Meropenem3	0.236	0.0
Vancomycin16	0.297	0.0
Rv2680_day32	0.21	0.0
H37Rv_KO_MarP	0.353	0.0
hypoxia_3wks	0.132	0.0
hypoxia_6wks	0.086	0.0
glycerol	-0.377	0.385
cholesterol	1.811	3.545
AJ	-0.281	0.0
Bibs02	-0.342	0.0
Bibs02c	0.867	0.0
BL6	-0.792	0.0
BL6a	0.423	0.0
BXD01	-0.77	0.0
BXD010	-0.141	0.0
BXD011	-0.328	0.0
BXD03	-0.599	0.0
BXD04	-0.156	0.0
BXD05	-0.677	0.0
BXD06	0.156	0.0
BXD07	-0.259	0.0
BXD08	0.103	0.0
BXD09	-0.458	0.0
CAST	-0.47	0.0
CCcont	-0.973	0.0
DS01	-0.4	0.0
DS02	-0.917	0.0
DS04	0.252	0.0
DS0c	-0.127	0.0
GP01	-1.167	0.0
GP02	0.142	0.0
GP0c	-0.98	0.0
NOD	-0.155	0.0
NZO	-0.241	0.0
PWK	0.45	0.0
H37Rv_KO_CtpC	-0.639	0.0
H37Rv_KO_CtpD	-0.759	0.0
H37Rv_KO_Rv1272	-1.334	0.0
H37Rv_KO_SugABC	-0.141	0.0
H37Rv_KO_MbtN	-0.518	0.0
Trans05	0.096	0.0
macrophage_unactivated	-0.71	0.0
IL1	-0.332	0.0
Rapamycin	0.129	0.0
Tcell	-0.313	0.0
GMCSF	0.222	0.0
IFNab	-0.178	0.0
IFNg	0.486	0.0
IFNg_GMCSF1	-0.424	0.0
Rv1432_day32	0.368	0.0
Rv1565c_day32	-0.393	0.0
secA2_input	0.387	0.847
delta_Rv3594	-0.489	0.0
delta_Rv3717	-0.148	0.0
delta_Rv3811	0.064	0.0
delta_Rv0954	-0.012	0.0
PonA1	-0.965	0.0
EccD1_KO	-0.105	0.0
EspI_KO	-0.448	0.0
PE35_KO	0.0	0.0
PPE68_KO	-0.179	0.0
glycerol2	-0.454	0.0
lignocerate	-0.369	0.0
oleate	-0.096	0.0
phosphatidylcholine	-0.368	0.0
acetate	-1.122	0.0
glucAc	-0.605	0.0
Rv0950ko	-0.618	0.0
Rv1096ko	-0.118	0.0
Rv3684ko	-0.154	0.0
delta_otsA_trehalose	-0.113	0.133