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 Rv1200/-:

update plot	correlation	link to info on gene
Rv0327c/cyp135A1	(cc=0.5344)	info on Rv0327c/cyp135A1
Rv0843/-	(cc=0.5215)	info on Rv0843/-
Rv0906/-	(cc=0.5156)	info on Rv0906/-
Rv0488/-	(cc=0.5069)	info on Rv0488/-
Rv1087A/-	(cc=0.5033)	info on Rv1087A/-
Rv2675c/-	(cc=0.4877)	info on Rv2675c/-
Rv0790c/-	(cc=0.4862)	info on Rv0790c/-
Rv0617/vapC29	(cc=0.4844)	info on Rv0617/vapC29
Rv3096/-	(cc=0.4687)	info on Rv3096/-
Rv3094c/-	(cc=0.4609)	info on Rv3094c/-

Correlation of Rv1200/- with Rv0843/-

Normalized LFCs for Rv1200/-:
(description and provenance of datasets)

	Rv1200/-	Rv0843/-
Fe_supp_jason_reseq	0.126	-0.117
low_pH_jason_reseq	-0.236	-0.505
NO_jason_reseq	0.097	-0.042
B6_jason_reseq	0.573	0.661
MHCII_jason_reseq	1.227	1.079
Isoniazid02	-0.611	-1.43
Rifampicin4	-0.233	0.355
Ethambutol3	-0.268	-1.085
Meropenem3	-0.289	-1.118
Vancomycin16	-0.769	-0.78
Rv2680_day32	-0.677	-0.745
H37Rv_KO_MarP	-0.027	0.0
hypoxia_3wks	0.044	0.088
hypoxia_6wks	-0.058	-0.263
glycerol	-0.383	-1.147
cholesterol	-0.156	-0.203
AJ	-0.084	0.269
Bibs02	0.51	0.095
Bibs02c	0.399	0.335
BL6	0.419	-0.302
BL6a	0.284	-0.158
BXD01	0.021	-0.672
BXD010	-0.324	-0.34
BXD011	0.02	-0.265
BXD03	0.093	-0.632
BXD04	0.215	-0.57
BXD05	0.551	-0.305
BXD06	-0.075	-0.258
BXD07	0.237	-0.931
BXD08	0.087	-0.485
BXD09	-0.109	-0.459
CAST	0.167	-0.035
CCcont	0.035	-0.568
DS01	0.512	0.484
DS02	0.436	-0.129
DS04	0.119	0.573
DS0c	0.663	-0.39
GP01	-0.574	-0.707
GP02	0.013	1.0
GP0c	-0.199	-0.639
NOD	0.33	0.67
NZO	0.501	-0.305
PWK	0.128	0.067
H37Rv_KO_CtpC	-0.293	-0.192
H37Rv_KO_CtpD	0.417	-0.045
H37Rv_KO_Rv1272	0.178	-0.584
H37Rv_KO_SugABC	0.479	-0.229
H37Rv_KO_MbtN	0.779	0.317
Trans05	0.036	0.296
macrophage_unactivated	0.549	-0.42
IL1	0.018	-0.119
Rapamycin	-0.052	1.016
Tcell	0.248	-0.404
GMCSF	0.42	-0.021
IFNab	0.23	0.048
IFNg	0.233	-0.064
IFNg_GMCSF1	0.273	0.336
Rv1432_day32	0.216	0.641
Rv1565c_day32	0.174	0.194
secA2_input	0.106	-0.117
delta_Rv3594	-0.346	0.659
delta_Rv3717	0.0	0.336
delta_Rv3811	0.028	0.15
delta_Rv0954	-0.292	0.464
PonA1	-0.052	0.893
EccD1_KO	0.122	1.309
EspI_KO	0.334	0.511
PE35_KO	0.54	0.111
PPE68_KO	0.739	0.122
glycerol2	0.853	0.765
lignocerate	0.706	0.799
oleate	0.44	0.517
phosphatidylcholine	0.926	0.755
acetate	0.426	0.441
glucAc	0.731	0.458
Rv0950ko	0.317	0.47
Rv1096ko	0.44	0.679
Rv3684ko	0.57	0.357
delta_otsA_trehalose	-0.776	-1.238