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 Rv2960c/-

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

	Rv3172c/-	Rv2960c/-
Fe_supp_jason_reseq	0.672	1.135
low_pH_jason_reseq	-0.617	-1.29
NO_jason_reseq	0.32	-0.756
B6_jason_reseq	0.496	1.024
MHCII_jason_reseq	0.991	0.959
Isoniazid02	1.98	-0.287
Rifampicin4	0.032	0.084
Ethambutol3	1.927	1.799
Meropenem3	-0.966	-0.775
Vancomycin16	-0.485	-0.276
Rv2680_day32	0.157	1.608
H37Rv_KO_MarP	0.08	-1.116
hypoxia_3wks	-0.423	-0.048
hypoxia_6wks	-0.459	-1.029
glycerol	-2.279	-0.835
cholesterol	-0.317	-0.459
AJ	-0.983	-0.55
Bibs02	-0.061	-1.057
Bibs02c	0.055	0.929
BL6	0.471	0.902
BL6a	0.303	0.656
BXD01	0.25	0.378
BXD010	-0.433	-0.228
BXD011	-0.087	0.649
BXD03	0.324	0.612
BXD04	-0.119	0.777
BXD05	0.438	0.767
BXD06	0.421	-0.144
BXD07	-0.216	0.97
BXD08	0.445	0.666
BXD09	0.124	0.493
CAST	0.118	-0.145
CCcont	0.662	1.087
DS01	0.106	0.033
DS02	-0.547	-0.709
DS04	-0.052	0.708
DS0c	-0.338	0.225
GP01	0.644	0.039
GP02	-0.369	0.907
GP0c	-0.089	-0.082
NOD	0.317	0.799
NZO	-0.387	-1.351
PWK	-0.629	-0.182
H37Rv_KO_CtpC	0.293	0.692
H37Rv_KO_CtpD	0.472	0.59
H37Rv_KO_Rv1272	0.141	1.133
H37Rv_KO_SugABC	-0.43	1.602
H37Rv_KO_MbtN	0.0	-0.726
Trans05	0.858	-0.181
macrophage_unactivated	-0.341	0.521
IL1	-0.635	0.119
Rapamycin	0.132	-0.574
Tcell	0.378	0.215
GMCSF	0.0	0.325
IFNab	-0.354	-0.166
IFNg	0.203	0.409
IFNg_GMCSF1	1.351	1.002
Rv1432_day32	-0.162	0.3
Rv1565c_day32	-0.153	0.444
secA2_input	-0.042	-1.262
delta_Rv3594	-0.493	0.541
delta_Rv3717	-0.773	0.573
delta_Rv3811	-0.375	0.677
delta_Rv0954	-0.447	1.623
PonA1	-0.532	0.502
EccD1_KO	-0.493	1.48
EspI_KO	-0.359	0.582
PE35_KO	0.423	0.755
PPE68_KO	0.56	0.998
glycerol2	0.5	1.892
lignocerate	1.199	2.72
oleate	-0.191	-0.829
phosphatidylcholine	0.725	1.982
acetate	0.918	2.555
glucAc	0.955	2.555
Rv0950ko	-0.769	-1.025
Rv1096ko	-0.341	0.332
Rv3684ko	-0.521	-0.108
delta_otsA_trehalose	-0.074	0.347