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 Rv3172c/-:

update plot	correlation	link to info on gene
Rv3747/-	(cc=0.5001)	info on Rv3747/-
Rv2960c/-	(cc=0.4806)	info on Rv2960c/-
Rv3174/-	(cc=0.4735)	info on Rv3174/-
Rv0854/-	(cc=0.468)	info on Rv0854/-
Rv1290c/-	(cc=0.4656)	info on Rv1290c/-
Rv2958c/-	(cc=0.4401)	info on Rv2958c/-
Rv2809/-	(cc=0.435)	info on Rv2809/-
Rv2970A/-	(cc=0.4304)	info on Rv2970A/-
Rv3660c/-	(cc=0.4285)	info on Rv3660c/-
Rv1915/aceAa	(cc=0.4157)	info on Rv1915/aceAa

Correlation of Rv3172c/- with Rv2958c/-

Normalized LFCs for Rv3172c/-:
(description and provenance of datasets)

	Rv3172c/-	Rv2958c/-
Fe_supp_jason_reseq	0.672	0.218
low_pH_jason_reseq	-0.617	-0.591
NO_jason_reseq	0.32	-0.412
B6_jason_reseq	0.496	-0.317
MHCII_jason_reseq	0.991	0.082
Isoniazid02	1.98	0.674
Rifampicin4	0.032	0.103
Ethambutol3	1.927	0.818
Meropenem3	-0.966	0.367
Vancomycin16	-0.485	0.257
Rv2680_day32	0.157	0.459
H37Rv_KO_MarP	0.08	0.464
hypoxia_3wks	-0.423	0.016
hypoxia_6wks	-0.459	-0.495
glycerol	-2.279	-1.678
cholesterol	-0.317	-0.524
AJ	-0.983	0.212
Bibs02	-0.061	0.257
Bibs02c	0.055	0.382
BL6	0.471	-0.448
BL6a	0.303	0.211
BXD01	0.25	-0.022
BXD010	-0.433	0.164
BXD011	-0.087	0.071
BXD03	0.324	-0.041
BXD04	-0.119	0.179
BXD05	0.438	0.198
BXD06	0.421	-0.162
BXD07	-0.216	-0.105
BXD08	0.445	0.008
BXD09	0.124	-0.21
CAST	0.118	0.092
CCcont	0.662	-0.071
DS01	0.106	0.269
DS02	-0.547	0.263
DS04	-0.052	0.548
DS0c	-0.338	0.225
GP01	0.644	0.408
GP02	-0.369	0.959
GP0c	-0.089	-0.35
NOD	0.317	0.937
NZO	-0.387	0.475
PWK	-0.629	0.485
H37Rv_KO_CtpC	0.293	0.377
H37Rv_KO_CtpD	0.472	0.694
H37Rv_KO_Rv1272	0.141	0.96
H37Rv_KO_SugABC	-0.43	0.495
H37Rv_KO_MbtN	0.0	0.425
Trans05	0.858	1.058
macrophage_unactivated	-0.341	0.136
IL1	-0.635	-0.744
Rapamycin	0.132	-0.276
Tcell	0.378	-0.306
GMCSF	0.0	-0.177
IFNab	-0.354	-0.414
IFNg	0.203	-0.179
IFNg_GMCSF1	1.351	0.277
Rv1432_day32	-0.162	0.365
Rv1565c_day32	-0.153	0.303
secA2_input	-0.042	-0.524
delta_Rv3594	-0.493	0.366
delta_Rv3717	-0.773	-0.198
delta_Rv3811	-0.375	0.26
delta_Rv0954	-0.447	-0.059
PonA1	-0.532	-0.108
EccD1_KO	-0.493	0.28
EspI_KO	-0.359	0.342
PE35_KO	0.423	0.586
PPE68_KO	0.56	0.394
glycerol2	0.5	0.509
lignocerate	1.199	0.6
oleate	-0.191	0.509
phosphatidylcholine	0.725	0.71
acetate	0.918	0.166
glucAc	0.955	0.194
Rv0950ko	-0.769	0.066
Rv1096ko	-0.341	-0.682
Rv3684ko	-0.521	-0.465
delta_otsA_trehalose	-0.074	0.014