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 Rv2715/-:

update plot	correlation	link to info on gene
Rv2394/ggtB	(cc=0.6425)	info on Rv2394/ggtB
Rv0338c/-	(cc=0.5414)	info on Rv0338c/-
Rv2268c/cyp128	(cc=0.4909)	info on Rv2268c/cyp128
Rv2189c/-	(cc=0.4775)	info on Rv2189c/-
Rv0373c/-	(cc=0.4709)	info on Rv0373c/-
Rv1317c/alkA	(cc=0.4611)	info on Rv1317c/alkA
Rv3730c/-	(cc=0.4507)	info on Rv3730c/-
Rv0069c/sdaA	(cc=0.4477)	info on Rv0069c/sdaA
Rv2962c/-	(cc=0.437)	info on Rv2962c/-
Rv0797/-	(cc=0.4327)	info on Rv0797/-

Correlation of Rv2715/- with Rv0338c/-

Normalized LFCs for Rv2715/-:
(description and provenance of datasets)

	Rv2715/-	Rv0338c/-
Fe_supp_jason_reseq	-0.508	0.0
low_pH_jason_reseq	0.796	0.0
NO_jason_reseq	-0.646	0.0
B6_jason_reseq	-0.542	0.0
MHCII_jason_reseq	0.346	0.0
Isoniazid02	1.224	0.0
Rifampicin4	-0.504	0.0
Ethambutol3	2.932	0.0
Meropenem3	2.498	0.0
Vancomycin16	0.0	0.0
Rv2680_day32	-0.73	0.0
H37Rv_KO_MarP	0.223	0.0
hypoxia_3wks	-0.116	0.0
hypoxia_6wks	0.175	0.0
glycerol	-0.471	0.385
cholesterol	4.799	3.545
AJ	-0.024	0.0
Bibs02	-0.223	0.0
Bibs02c	1.516	0.0
BL6	0.26	0.0
BL6a	1.24	0.0
BXD01	0.314	0.0
BXD010	1.166	0.0
BXD011	0.642	0.0
BXD03	0.349	0.0
BXD04	0.809	0.0
BXD05	0.369	0.0
BXD06	0.366	0.0
BXD07	0.357	0.0
BXD08	0.448	0.0
BXD09	0.788	0.0
CAST	-0.28	0.0
CCcont	0.348	0.0
DS01	0.429	0.0
DS02	0.132	0.0
DS04	0.682	0.0
DS0c	0.046	0.0
GP01	0.804	0.0
GP02	0.516	0.0
GP0c	0.387	0.0
NOD	1.787	0.0
NZO	-0.964	0.0
PWK	0.158	0.0
H37Rv_KO_CtpC	0.607	0.0
H37Rv_KO_CtpD	0.185	0.0
H37Rv_KO_Rv1272	0.558	0.0
H37Rv_KO_SugABC	0.898	0.0
H37Rv_KO_MbtN	1.101	0.0
Trans05	1.278	0.0
macrophage_unactivated	0.3	0.0
IL1	-0.065	0.0
Rapamycin	0.353	0.0
Tcell	0.176	0.0
GMCSF	-0.148	0.0
IFNab	-0.133	0.0
IFNg	0.644	0.0
IFNg_GMCSF1	-0.358	0.0
Rv1432_day32	-0.499	0.0
Rv1565c_day32	-0.655	0.0
secA2_input	-0.11	0.847
delta_Rv3594	0.728	0.0
delta_Rv3717	0.151	0.0
delta_Rv3811	1.169	0.0
delta_Rv0954	0.783	0.0
PonA1	0.386	0.0
EccD1_KO	1.095	0.0
EspI_KO	0.95	0.0
PE35_KO	1.476	0.0
PPE68_KO	0.784	0.0
glycerol2	-0.476	0.0
lignocerate	0.102	0.0
oleate	-0.216	0.0
phosphatidylcholine	0.0	0.0
acetate	0.206	0.0
glucAc	0.481	0.0
Rv0950ko	-0.109	0.0
Rv1096ko	-0.145	0.0
Rv3684ko	-0.318	0.0
delta_otsA_trehalose	0.879	0.133