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 Rv1817/-:

update plot	correlation	link to info on gene
Rv2113/-	(cc=0.8479)	info on Rv2113/-
Rv0453/PPE11	(cc=0.8091)	info on Rv0453/PPE11
Rv2848c/cobB	(cc=0.7965)	info on Rv2848c/cobB
Rv2822c/-	(cc=0.7829)	info on Rv2822c/-
Rv0159c/PE3	(cc=0.7688)	info on Rv0159c/PE3
Rv3815c/-	(cc=0.7673)	info on Rv3815c/-
Rv3862c/whiB6	(cc=0.5436)	info on Rv3862c/whiB6
Rv2339/mmpL9	(cc=0.5212)	info on Rv2339/mmpL9
Rv3685c/cyp137	(cc=0.5029)	info on Rv3685c/cyp137
Rv2389c/rpfD	(cc=0.5017)	info on Rv2389c/rpfD

Correlation of Rv1817/- with Rv2339/mmpL9

Normalized LFCs for Rv1817/-:
(description and provenance of datasets)

	Rv1817/-	Rv2339/mmpL9
Fe_supp_jason_reseq	-0.223	0.283
low_pH_jason_reseq	-0.388	-0.164
NO_jason_reseq	-0.714	-0.349
B6_jason_reseq	-0.232	-0.289
MHCII_jason_reseq	0.326	0.481
Isoniazid02	0.215	0.375
Rifampicin4	0.0	0.0
Ethambutol3	0.612	0.568
Meropenem3	0.316	-0.052
Vancomycin16	-0.04	0.146
Rv2680_day32	-0.437	0.365
H37Rv_KO_MarP	-0.186	0.047
hypoxia_3wks	0.116	0.267
hypoxia_6wks	-0.203	-0.177
glycerol	0.604	-0.426
cholesterol	0.241	-0.305
AJ	-0.311	0.247
Bibs02	0.738	-0.127
Bibs02c	0.358	-0.276
BL6	-0.327	0.196
BL6a	-0.133	0.211
BXD01	0.177	0.253
BXD010	-0.209	0.557
BXD011	0.092	0.394
BXD03	-0.113	0.36
BXD04	-0.103	0.565
BXD05	-0.219	0.615
BXD06	0.007	0.413
BXD07	-0.344	0.295
BXD08	0.091	0.087
BXD09	-0.331	0.41
CAST	0.22	0.404
CCcont	-0.371	-0.197
DS01	0.453	0.154
DS02	0.334	-0.126
DS04	0.332	0.6
DS0c	0.409	0.578
GP01	-0.077	0.591
GP02	0.301	0.138
GP0c	-0.088	0.057
NOD	0.441	1.289
NZO	0.069	0.35
PWK	0.068	0.47
H37Rv_KO_CtpC	0.111	0.488
H37Rv_KO_CtpD	0.178	0.668
H37Rv_KO_Rv1272	1.0	1.099
H37Rv_KO_SugABC	-0.144	0.751
H37Rv_KO_MbtN	0.43	0.571
Trans05	1.011	1.072
macrophage_unactivated	1.588	0.42
IL1	2.201	0.611
Rapamycin	2.317	0.724
Tcell	-4.923	-0.648
GMCSF	2.26	1.225
IFNab	1.886	0.801
IFNg	2.397	1.056
IFNg_GMCSF1	2.385	0.55
Rv1432_day32	0.096	0.576
Rv1565c_day32	-0.156	0.3
secA2_input	-0.434	-0.631
delta_Rv3594	0.0	-0.072
delta_Rv3717	-0.028	0.0
delta_Rv3811	0.28	0.046
delta_Rv0954	0.142	0.079
PonA1	-0.059	-0.293
EccD1_KO	0.687	-0.046
EspI_KO	0.359	-0.168
PE35_KO	0.63	0.166
PPE68_KO	0.56	0.355
glycerol2	0.085	0.0
lignocerate	-0.069	0.339
oleate	0.386	0.081
phosphatidylcholine	0.239	0.231
acetate	-0.156	-0.048
glucAc	-0.167	-0.227
Rv0950ko	0.13	0.121
Rv1096ko	-0.392	-1.095
Rv3684ko	-0.102	-0.223
delta_otsA_trehalose	-0.085	-0.557