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 Rv1208/gpgS

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

	Rv3004/cfp6	Rv1208/gpgS
Fe_supp_jason_reseq	-1.746	0.0
low_pH_jason_reseq	-2.802	0.0
NO_jason_reseq	-0.215	0.0
B6_jason_reseq	1.311	0.0
MHCII_jason_reseq	-0.604	0.0
Isoniazid02	-0.308	0.0
Rifampicin4	0.23	0.0
Ethambutol3	-0.711	0.0
Meropenem3	-0.624	0.0
Vancomycin16	0.114	0.0
Rv2680_day32	0.131	0.0
H37Rv_KO_MarP	-0.845	0.0
hypoxia_3wks	-0.231	0.0
hypoxia_6wks	0.541	0.0
glycerol	0.471	0.0
cholesterol	-0.156	0.0
AJ	0.834	0.0
Bibs02	1.317	0.0
Bibs02c	-0.406	0.0
BL6	-0.49	0.0
BL6a	0.888	0.0
BXD01	0.352	0.0
BXD010	-0.728	0.0
BXD011	0.491	0.0
BXD03	0.085	0.0
BXD04	0.395	0.0
BXD05	0.43	0.0
BXD06	-0.418	0.0
BXD07	0.0	0.0
BXD08	0.013	0.0
BXD09	0.938	0.0
CAST	0.991	0.0
CCcont	0.0	0.149
DS01	1.711	0.0
DS02	1.418	0.0
DS04	-0.271	0.0
DS0c	1.738	0.0
GP01	-0.309	0.0
GP02	-1.639	0.0
GP0c	-1.209	0.0
NOD	0.142	0.0
NZO	2.068	0.0
PWK	-0.404	0.0
H37Rv_KO_CtpC	-3.53	0.0
H37Rv_KO_CtpD	-2.851	0.0
H37Rv_KO_Rv1272	-0.124	0.0
H37Rv_KO_SugABC	-2.014	0.0
H37Rv_KO_MbtN	-0.417	0.0
Trans05	-0.807	0.0
macrophage_unactivated	0.492	0.0
IL1	0.039	0.0
Rapamycin	0.813	0.0
Tcell	2.095	0.0
GMCSF	0.29	0.0
IFNab	0.366	0.0
IFNg	2.245	0.0
IFNg_GMCSF1	0.233	0.0
Rv1432_day32	-1.079	0.0
Rv1565c_day32	-1.229	0.0
secA2_input	-3.611	-1.234
delta_Rv3594	1.869	0.0
delta_Rv3717	0.405	0.0
delta_Rv3811	1.096	0.0
delta_Rv0954	1.613	0.178
PonA1	2.748	0.0
EccD1_KO	3.983	0.454
EspI_KO	4.195	1.383
PE35_KO	3.209	2.234
PPE68_KO	2.003	2.451
glycerol2	0.834	0.0
lignocerate	0.952	0.0
oleate	0.948	0.0
phosphatidylcholine	0.466	0.0
acetate	0.457	0.0
glucAc	0.415	0.272
Rv0950ko	1.061	0.416
Rv1096ko	2.147	0.416
Rv3684ko	0.567	1.241
delta_otsA_trehalose	-0.837	0.133