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 Rv3004/cfp6:

update plot	correlation	link to info on gene
Rv0895/-	(cc=0.5039)	info on Rv0895/-
Rv0800/pepC	(cc=0.4928)	info on Rv0800/pepC
Rv1208/gpgS	(cc=0.4856)	info on Rv1208/gpgS
Rv0664/vapB8	(cc=0.4727)	info on Rv0664/vapB8
Rv1023/eno	(cc=0.4695)	info on Rv1023/eno
Rv1125/-	(cc=0.4613)	info on Rv1125/-
Rv1638A/-	(cc=0.4537)	info on Rv1638A/-
Rv0306/-	(cc=0.4519)	info on Rv0306/-
Rv2307D/-	(cc=0.4389)	info on Rv2307D/-
Rv1136/-	(cc=0.4378)	info on Rv1136/-

Correlation of Rv3004/cfp6 with Rv0895/-

Normalized LFCs for Rv3004/cfp6:
(description and provenance of datasets)

	Rv3004/cfp6	Rv0895/-
Fe_supp_jason_reseq	-1.746	-0.625
low_pH_jason_reseq	-2.802	-1.121
NO_jason_reseq	-0.215	-0.583
B6_jason_reseq	1.311	0.36
MHCII_jason_reseq	-0.604	-0.008
Isoniazid02	-0.308	-0.565
Rifampicin4	0.23	0.661
Ethambutol3	-0.711	-0.19
Meropenem3	-0.624	0.655
Vancomycin16	0.114	0.117
Rv2680_day32	0.131	0.213
H37Rv_KO_MarP	-0.845	0.294
hypoxia_3wks	-0.231	0.227
hypoxia_6wks	0.541	0.267
glycerol	0.471	0.129
cholesterol	-0.156	0.287
AJ	0.834	0.213
Bibs02	1.317	0.4
Bibs02c	-0.406	0.164
BL6	-0.49	-0.282
BL6a	0.888	-0.092
BXD01	0.352	-0.245
BXD010	-0.728	-0.416
BXD011	0.491	-0.477
BXD03	0.085	-0.375
BXD04	0.395	-0.263
BXD05	0.43	-0.143
BXD06	-0.418	-0.02
BXD07	0.0	-0.384
BXD08	0.013	-0.007
BXD09	0.938	-0.166
CAST	0.991	0.953
CCcont	0.0	-0.625
DS01	1.711	0.775
DS02	1.418	0.824
DS04	-0.271	0.479
DS0c	1.738	0.955
GP01	-0.309	-0.111
GP02	-1.639	0.084
GP0c	-1.209	-0.496
NOD	0.142	0.387
NZO	2.068	0.146
PWK	-0.404	0.57
H37Rv_KO_CtpC	-3.53	-0.377
H37Rv_KO_CtpD	-2.851	-0.579
H37Rv_KO_Rv1272	-0.124	-0.391
H37Rv_KO_SugABC	-2.014	-0.243
H37Rv_KO_MbtN	-0.417	-0.232
Trans05	-0.807	-0.547
macrophage_unactivated	0.492	-0.84
IL1	0.039	0.172
Rapamycin	0.813	0.227
Tcell	2.095	0.026
GMCSF	0.29	-0.322
IFNab	0.366	-0.236
IFNg	2.245	0.342
IFNg_GMCSF1	0.233	0.079
Rv1432_day32	-1.079	-0.076
Rv1565c_day32	-1.229	0.594
secA2_input	-3.611	0.036
delta_Rv3594	1.869	-0.629
delta_Rv3717	0.405	0.033
delta_Rv3811	1.096	-0.207
delta_Rv0954	1.613	-0.017
PonA1	2.748	0.554
EccD1_KO	3.983	0.539
EspI_KO	4.195	1.323
PE35_KO	3.209	0.478
PPE68_KO	2.003	0.637
glycerol2	0.834	0.154
lignocerate	0.952	0.145
oleate	0.948	0.169
phosphatidylcholine	0.466	0.251
acetate	0.457	0.0
glucAc	0.415	0.492
Rv0950ko	1.061	-0.302
Rv1096ko	2.147	0.341
Rv3684ko	0.567	-0.557
delta_otsA_trehalose	-0.837	-0.358