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 Rv1469/ctpD:

update plot	correlation	link to info on gene
Rv0209/-	(cc=0.4705)	info on Rv0209/-
Rv1045/-	(cc=0.4476)	info on Rv1045/-
Rv2789c/fadE21	(cc=0.4457)	info on Rv2789c/fadE21
Rv3386/-	(cc=0.4363)	info on Rv3386/-
Rv1755c/plcD	(cc=0.4209)	info on Rv1755c/plcD
Rv1954c/-	(cc=0.4206)	info on Rv1954c/-
Rv2617c/-	(cc=0.4184)	info on Rv2617c/-
Rv2481c/-	(cc=0.409)	info on Rv2481c/-
Rv1038c/esxJ	(cc=0.4049)	info on Rv1038c/esxJ
Rv2587c/secD	(cc=0.4042)	info on Rv2587c/secD

Correlation of Rv1469/ctpD with Rv0209/-

Normalized LFCs for Rv1469/ctpD:
(description and provenance of datasets)

	Rv1469/ctpD	Rv0209/-
Fe_supp_jason_reseq	0.152	-0.426
low_pH_jason_reseq	-1.591	-0.428
NO_jason_reseq	0.252	-0.528
B6_jason_reseq	-0.259	-0.729
MHCII_jason_reseq	-0.547	-0.108
Isoniazid02	0.422	0.569
Rifampicin4	0.032	0.528
Ethambutol3	0.388	0.415
Meropenem3	-0.155	0.019
Vancomycin16	0.191	0.085
Rv2680_day32	0.284	0.802
H37Rv_KO_MarP	-0.038	0.697
hypoxia_3wks	-0.191	0.478
hypoxia_6wks	0.033	-0.71
glycerol	0.246	0.984
cholesterol	-0.452	0.214
AJ	-0.617	-0.877
Bibs02	-0.11	0.372
Bibs02c	-0.153	-1.381
BL6	0.085	0.621
BL6a	-0.527	-0.535
BXD01	0.075	-0.108
BXD010	-0.061	0.16
BXD011	-0.547	-0.281
BXD03	0.273	0.746
BXD04	-0.488	0.331
BXD05	-0.259	0.413
BXD06	0.031	0.0
BXD07	-0.229	0.327
BXD08	0.105	0.341
BXD09	-0.374	0.301
CAST	0.42	0.494
CCcont	0.243	0.058
DS01	-0.358	0.031
DS02	0.354	0.057
DS04	-1.522	0.242
DS0c	-0.481	0.167
GP01	0.988	1.634
GP02	0.863	1.078
GP0c	0.625	1.256
NOD	0.721	0.306
NZO	-1.12	-1.22
PWK	-0.27	-0.669
H37Rv_KO_CtpC	0.198	0.105
H37Rv_KO_CtpD	-0.818	-0.806
H37Rv_KO_Rv1272	-0.085	0.527
H37Rv_KO_SugABC	-1.655	-0.474
H37Rv_KO_MbtN	-0.538	0.276
Trans05	0.374	0.309
macrophage_unactivated	0.177	-0.628
IL1	-0.353	0.946
Rapamycin	0.172	0.703
Tcell	-0.254	-0.424
GMCSF	-0.776	0.57
IFNab	0.0	1.037
IFNg	-0.371	1.521
IFNg_GMCSF1	0.06	-0.251
Rv1432_day32	0.455	1.707
Rv1565c_day32	0.096	0.824
secA2_input	-1.606	0.322
delta_Rv3594	-0.384	-1.325
delta_Rv3717	-0.459	-0.49
delta_Rv3811	-0.094	-0.22
delta_Rv0954	-0.472	0.026
PonA1	0.379	0.247
EccD1_KO	-0.145	-0.414
EspI_KO	-0.676	-1.486
PE35_KO	-0.128	-0.677
PPE68_KO	-0.493	-0.848
glycerol2	0.46	0.887
lignocerate	0.57	1.087
oleate	0.064	1.151
phosphatidylcholine	0.608	0.662
acetate	0.399	0.923
glucAc	1.17	0.694
Rv0950ko	0.093	0.139
Rv1096ko	0.142	0.778
Rv3684ko	1.461	0.151
delta_otsA_trehalose	-0.724	-2.114