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 Rv2562/-:

update plot	correlation	link to info on gene
Rv2276/cyp121	(cc=0.5556)	info on Rv2276/cyp121
Rv2833c/ugpB	(cc=0.5305)	info on Rv2833c/ugpB
Rv1954A/-	(cc=0.5253)	info on Rv1954A/-
Rv1526c/-	(cc=0.5193)	info on Rv1526c/-
Rv0698/-	(cc=0.4958)	info on Rv0698/-
Rv0792c/-	(cc=0.4799)	info on Rv0792c/-
Rv0349/-	(cc=0.4789)	info on Rv0349/-
Rv2253/-	(cc=0.4763)	info on Rv2253/-
Rv2040c/-	(cc=0.4693)	info on Rv2040c/-
Rv3429/PPE59	(cc=0.4624)	info on Rv3429/PPE59

Correlation of Rv2562/- with Rv2276/cyp121

Normalized LFCs for Rv2562/-:
(description and provenance of datasets)

	Rv2562/-	Rv2276/cyp121
Fe_supp_jason_reseq	-0.226	0.439
low_pH_jason_reseq	-0.87	-0.052
NO_jason_reseq	-0.386	-0.806
B6_jason_reseq	-1.875	-0.341
MHCII_jason_reseq	-0.528	0.367
Isoniazid02	0.224	-0.042
Rifampicin4	0.441	-0.241
Ethambutol3	0.045	-0.306
Meropenem3	0.401	-0.474
Vancomycin16	0.647	0.223
Rv2680_day32	0.503	-0.449
H37Rv_KO_MarP	0.422	-0.26
hypoxia_3wks	-0.471	-0.403
hypoxia_6wks	0.044	-1.247
glycerol	-1.226	0.237
cholesterol	-0.097	0.233
AJ	-0.022	1.133
Bibs02	0.743	0.55
Bibs02c	-1.088	-0.277
BL6	0.954	1.637
BL6a	-0.293	0.936
BXD01	0.195	1.007
BXD010	0.7	0.564
BXD011	0.647	0.581
BXD03	0.533	1.281
BXD04	0.614	1.013
BXD05	0.613	0.888
BXD06	1.012	1.393
BXD07	0.602	0.491
BXD08	0.675	1.581
BXD09	0.787	1.36
CAST	0.719	0.42
CCcont	0.349	1.89
DS01	-0.44	0.479
DS02	-0.05	0.158
DS04	0.658	0.472
DS0c	0.209	0.693
GP01	0.295	0.678
GP02	0.362	-0.384
GP0c	0.024	0.094
NOD	1.036	1.988
NZO	-0.275	0.097
PWK	0.371	0.142
H37Rv_KO_CtpC	0.923	1.918
H37Rv_KO_CtpD	1.291	0.516
H37Rv_KO_Rv1272	0.843	0.931
H37Rv_KO_SugABC	0.168	1.332
H37Rv_KO_MbtN	-0.83	-0.108
Trans05	1.309	1.265
macrophage_unactivated	1.446	0.859
IL1	0.528	-0.617
Rapamycin	0.712	-0.338
Tcell	0.613	0.541
GMCSF	0.04	-0.444
IFNab	-0.339	-0.109
IFNg	0.858	0.045
IFNg_GMCSF1	0.575	-0.226
Rv1432_day32	-0.332	-0.143
Rv1565c_day32	-0.423	-0.599
secA2_input	-1.929	-1.486
delta_Rv3594	0.153	-0.623
delta_Rv3717	-0.077	-1.106
delta_Rv3811	0.125	0.44
delta_Rv0954	0.021	-0.441
PonA1	0.853	0.684
EccD1_KO	0.441	0.21
EspI_KO	0.476	2.193
PE35_KO	0.825	2.129
PPE68_KO	0.723	1.872
glycerol2	1.247	1.864
lignocerate	1.249	2.12
oleate	0.943	0.169
phosphatidylcholine	1.424	1.84
acetate	1.077	2.369
glucAc	0.617	1.957
Rv0950ko	-0.585	0.06
Rv1096ko	-0.368	0.06
Rv3684ko	0.079	-0.416
delta_otsA_trehalose	-0.634	1.275