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 Rv0063/-:

update plot	correlation	link to info on gene
Rv1675c/cmr	(cc=0.5603)	info on Rv1675c/cmr
Rv0669c/-	(cc=0.5197)	info on Rv0669c/-
Rv0338c/-	(cc=0.5024)	info on Rv0338c/-
Rv3283/sseA	(cc=0.4817)	info on Rv3283/sseA
Rv2268c/cyp128	(cc=0.4799)	info on Rv2268c/cyp128
Rv1371/-	(cc=0.4686)	info on Rv1371/-
Rv2431c/PE25	(cc=0.4568)	info on Rv2431c/PE25
Rv3509c/ilvX	(cc=0.4437)	info on Rv3509c/ilvX
Rv3154/nuoJ	(cc=0.4374)	info on Rv3154/nuoJ
Rv3529c/-	(cc=0.435)	info on Rv3529c/-

Correlation of Rv0063/- with Rv0338c/-

Normalized LFCs for Rv0063/-:
(description and provenance of datasets)

	Rv0063/-	Rv0338c/-
Fe_supp_jason_reseq	-0.568	0.0
low_pH_jason_reseq	-0.172	0.0
NO_jason_reseq	-0.026	0.0
B6_jason_reseq	0.872	0.0
MHCII_jason_reseq	0.139	0.0
Isoniazid02	-0.228	0.0
Rifampicin4	0.0	0.0
Ethambutol3	-0.134	0.0
Meropenem3	0.037	0.0
Vancomycin16	0.218	0.0
Rv2680_day32	-0.874	0.0
H37Rv_KO_MarP	0.775	0.0
hypoxia_3wks	-0.805	0.0
hypoxia_6wks	-0.24	0.0
glycerol	1.176	0.385
cholesterol	2.914	3.545
AJ	0.788	0.0
Bibs02	-0.029	0.0
Bibs02c	0.587	0.0
BL6	0.621	0.0
BL6a	0.43	0.0
BXD01	-0.098	0.0
BXD010	0.261	0.0
BXD011	0.587	0.0
BXD03	0.756	0.0
BXD04	0.354	0.0
BXD05	0.599	0.0
BXD06	0.043	0.0
BXD07	0.148	0.0
BXD08	0.011	0.0
BXD09	-0.046	0.0
CAST	0.516	0.0
CCcont	0.07	0.0
DS01	1.136	0.0
DS02	0.726	0.0
DS04	1.318	0.0
DS0c	0.662	0.0
GP01	0.201	0.0
GP02	-0.748	0.0
GP0c	-0.251	0.0
NOD	1.36	0.0
NZO	0.446	0.0
PWK	0.924	0.0
H37Rv_KO_CtpC	0.0	0.0
H37Rv_KO_CtpD	-0.283	0.0
H37Rv_KO_Rv1272	-0.233	0.0
H37Rv_KO_SugABC	0.942	0.0
H37Rv_KO_MbtN	0.276	0.0
Trans05	-0.548	0.0
macrophage_unactivated	-0.363	0.0
IL1	-0.053	0.0
Rapamycin	-0.835	0.0
Tcell	-0.606	0.0
GMCSF	0.166	0.0
IFNab	0.0	0.0
IFNg	-0.048	0.0
IFNg_GMCSF1	-0.088	0.0
Rv1432_day32	-0.089	0.0
Rv1565c_day32	0.351	0.0
secA2_input	0.095	0.847
delta_Rv3594	-0.159	0.0
delta_Rv3717	-0.458	0.0
delta_Rv3811	-0.607	0.0
delta_Rv0954	0.522	0.0
PonA1	0.658	0.0
EccD1_KO	-0.178	0.0
EspI_KO	-0.317	0.0
PE35_KO	0.271	0.0
PPE68_KO	0.266	0.0
glycerol2	0.048	0.0
lignocerate	0.664	0.0
oleate	-1.212	0.0
phosphatidylcholine	-0.253	0.0
acetate	0.484	0.0
glucAc	0.575	0.0
Rv0950ko	0.425	0.0
Rv1096ko	0.392	0.0
Rv3684ko	0.747	0.0
delta_otsA_trehalose	-0.535	0.133