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 Rv3744/nmtR:

update plot	correlation	link to info on gene
Rv0393/-	(cc=0.4691)	info on Rv0393/-
Rv0133/-	(cc=0.4681)	info on Rv0133/-
Rv3470c/ilvB2	(cc=0.4677)	info on Rv3470c/ilvB2
Rv3558/PPE64	(cc=0.4654)	info on Rv3558/PPE64
Rv3142c/-	(cc=0.4531)	info on Rv3142c/-
Rv3517/-	(cc=0.4522)	info on Rv3517/-
Rv0823c/-	(cc=0.4468)	info on Rv0823c/-
Rv3912/-	(cc=0.4437)	info on Rv3912/-
Rv2797c/-	(cc=0.4368)	info on Rv2797c/-
Rv3904c/esxE	(cc=0.4334)	info on Rv3904c/esxE

Correlation of Rv3744/nmtR with Rv2797c/-

Normalized LFCs for Rv3744/nmtR:
(description and provenance of datasets)

	Rv3744/nmtR	Rv2797c/-
Fe_supp_jason_reseq	-1.793	-0.38
low_pH_jason_reseq	-0.982	-1.114
NO_jason_reseq	0.134	-0.289
B6_jason_reseq	-1.443	-0.538
MHCII_jason_reseq	-0.96	0.394
Isoniazid02	0.23	0.146
Rifampicin4	0.111	-0.179
Ethambutol3	0.745	0.315
Meropenem3	0.298	0.0
Vancomycin16	0.162	0.151
Rv2680_day32	-1.045	0.947
H37Rv_KO_MarP	0.138	0.302
hypoxia_3wks	0.949	1.619
hypoxia_6wks	-0.831	1.608
glycerol	-0.025	0.439
cholesterol	0.079	0.163
AJ	1.198	0.565
Bibs02	-0.703	0.114
Bibs02c	-0.443	0.226
BL6	0.81	0.532
BL6a	-0.317	0.475
BXD01	0.426	0.189
BXD010	-0.481	0.165
BXD011	-0.149	0.112
BXD03	-0.042	0.391
BXD04	0.022	0.941
BXD05	0.049	0.303
BXD06	-0.377	0.467
BXD07	0.301	0.405
BXD08	0.499	0.16
BXD09	-0.017	0.366
CAST	0.429	0.601
CCcont	-0.186	-0.077
DS01	-0.744	0.667
DS02	0.118	0.545
DS04	0.15	0.759
DS0c	0.278	0.464
GP01	0.809	0.843
GP02	0.245	0.603
GP0c	-0.1	0.626
NOD	0.804	0.618
NZO	0.643	0.419
PWK	1.65	0.834
H37Rv_KO_CtpC	1.471	0.61
H37Rv_KO_CtpD	1.334	0.242
H37Rv_KO_Rv1272	-0.053	-0.252
H37Rv_KO_SugABC	1.483	0.273
H37Rv_KO_MbtN	-0.806	-0.321
Trans05	0.485	0.299
macrophage_unactivated	-0.354	-0.155
IL1	-1.605	0.43
Rapamycin	-0.921	0.187
Tcell	-0.661	0.124
GMCSF	-0.734	-0.222
IFNab	-1.218	0.157
IFNg	-1.013	0.259
IFNg_GMCSF1	-0.028	0.016
Rv1432_day32	-1.276	-0.19
Rv1565c_day32	-0.174	-0.182
secA2_input	1.747	0.07
delta_Rv3594	-0.424	0.135
delta_Rv3717	-0.245	-0.053
delta_Rv3811	0.77	0.061
delta_Rv0954	-0.074	0.291
PonA1	1.046	0.756
EccD1_KO	-0.375	0.22
EspI_KO	-0.95	-0.183
PE35_KO	-1.342	-0.239
PPE68_KO	-2.166	-0.518
glycerol2	-0.34	-0.035
lignocerate	-0.801	-0.016
oleate	0.751	0.179
phosphatidylcholine	-0.34	0.069
acetate	-0.316	-0.598
glucAc	-0.992	-0.585
Rv0950ko	1.182	0.781
Rv1096ko	0.513	0.576
Rv3684ko	0.069	0.455
delta_otsA_trehalose	1.21	0.295