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 Rv1125/-

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

	Rv3004/cfp6	Rv1125/-
Fe_supp_jason_reseq	-1.746	-0.448
low_pH_jason_reseq	-2.802	0.167
NO_jason_reseq	-0.215	-0.428
B6_jason_reseq	1.311	0.929
MHCII_jason_reseq	-0.604	1.89
Isoniazid02	-0.308	-1.603
Rifampicin4	0.23	0.43
Ethambutol3	-0.711	-1.75
Meropenem3	-0.624	-1.635
Vancomycin16	0.114	-0.735
Rv2680_day32	0.131	-0.091
H37Rv_KO_MarP	-0.845	0.879
hypoxia_3wks	-0.231	0.443
hypoxia_6wks	0.541	0.34
glycerol	0.471	1.055
cholesterol	-0.156	-0.345
AJ	0.834	0.334
Bibs02	1.317	0.136
Bibs02c	-0.406	0.659
BL6	-0.49	0.832
BL6a	0.888	0.075
BXD01	0.352	0.274
BXD010	-0.728	-0.274
BXD011	0.491	-0.272
BXD03	0.085	-0.424
BXD04	0.395	0.298
BXD05	0.43	0.194
BXD06	-0.418	0.124
BXD07	0.0	-0.296
BXD08	0.013	0.214
BXD09	0.938	-0.204
CAST	0.991	-0.492
CCcont	0.0	0.533
DS01	1.711	1.369
DS02	1.418	0.685
DS04	-0.271	0.214
DS0c	1.738	1.328
GP01	-0.309	-0.284
GP02	-1.639	-0.635
GP0c	-1.209	-0.342
NOD	0.142	1.092
NZO	2.068	-0.678
PWK	-0.404	-0.038
H37Rv_KO_CtpC	-3.53	-0.387
H37Rv_KO_CtpD	-2.851	-1.696
H37Rv_KO_Rv1272	-0.124	0.444
H37Rv_KO_SugABC	-2.014	-0.575
H37Rv_KO_MbtN	-0.417	-1.245
Trans05	-0.807	0.049
macrophage_unactivated	0.492	0.0
IL1	0.039	0.721
Rapamycin	0.813	0.681
Tcell	2.095	-1.248
GMCSF	0.29	1.281
IFNab	0.366	0.142
IFNg	2.245	0.307
IFNg_GMCSF1	0.233	0.952
Rv1432_day32	-1.079	0.271
Rv1565c_day32	-1.229	-0.398
secA2_input	-3.611	-1.288
delta_Rv3594	1.869	0.698
delta_Rv3717	0.405	0.101
delta_Rv3811	1.096	-0.403
delta_Rv0954	1.613	0.053
PonA1	2.748	0.0
EccD1_KO	3.983	1.411
EspI_KO	4.195	1.104
PE35_KO	3.209	1.129
PPE68_KO	2.003	0.813
glycerol2	0.834	0.113
lignocerate	0.952	0.704
oleate	0.948	0.058
phosphatidylcholine	0.466	0.625
acetate	0.457	0.555
glucAc	0.415	0.311
Rv0950ko	1.061	0.793
Rv1096ko	2.147	0.995
Rv3684ko	0.567	0.632
delta_otsA_trehalose	-0.837	-0.147