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 Rv0206c/mmpL3:

update plot	correlation	link to info on gene
Rv0431/-	(cc=0.5592)	info on Rv0431/-
Rv3789/-	(cc=0.5076)	info on Rv3789/-
Rv2197c/-	(cc=0.4791)	info on Rv2197c/-
Rv0020c/fhaA	(cc=0.4677)	info on Rv0020c/fhaA
Rv3670/ephE	(cc=0.4598)	info on Rv3670/ephE
Rv2198c/mmpS3	(cc=0.4521)	info on Rv2198c/mmpS3
Rv0425c/ctpH	(cc=0.4518)	info on Rv0425c/ctpH
Rv1411c/lprG	(cc=0.4469)	info on Rv1411c/lprG
Rv0645c/mmaA1	(cc=0.4452)	info on Rv0645c/mmaA1
Rv3753c/-	(cc=0.445)	info on Rv3753c/-

Correlation of Rv0206c/mmpL3 with Rv3753c/-

Normalized LFCs for Rv0206c/mmpL3:
(description and provenance of datasets)

	Rv0206c/mmpL3	Rv3753c/-
Fe_supp_jason_reseq	0.0	1.778
low_pH_jason_reseq	0.0	0.582
NO_jason_reseq	0.0	-0.362
B6_jason_reseq	0.0	-0.153
MHCII_jason_reseq	0.135	0.0
Isoniazid02	-0.167	0.0
Rifampicin4	-0.653	0.0
Ethambutol3	-0.293	0.0
Meropenem3	-0.454	0.0
Vancomycin16	-1.005	0.0
Rv2680_day32	3.519	0.0
H37Rv_KO_MarP	-1.782	-0.255
hypoxia_3wks	0.0	0.0
hypoxia_6wks	0.0	0.0
glycerol	0.0	0.0
cholesterol	-0.145	0.0
AJ	-0.232	0.0
Bibs02	-0.183	0.0
Bibs02c	-0.209	0.0
BL6	-0.125	0.0
BL6a	-0.198	0.0
BXD01	-0.13	0.0
BXD010	-0.128	0.0
BXD011	-0.127	0.243
BXD03	-0.135	0.0
BXD04	-0.124	1.619
BXD05	-0.135	0.0
BXD06	-0.133	0.0
BXD07	-0.138	0.0
BXD08	-0.133	0.0
BXD09	-0.14	0.0
CAST	-0.23	0.0
CCcont	0.0	0.0
DS01	-0.236	0.0
DS02	-0.217	0.0
DS04	-0.194	0.0
DS0c	0.0	0.0
GP01	0.249	0.0
GP02	0.981	0.0
GP0c	-0.13	0.0
NOD	-0.225	0.0
NZO	-0.199	0.0
PWK	-0.196	0.0
H37Rv_KO_CtpC	0.148	0.0
H37Rv_KO_CtpD	-0.127	0.127
H37Rv_KO_Rv1272	-0.141	0.0
H37Rv_KO_SugABC	0.388	0.0
H37Rv_KO_MbtN	-0.103	0.0
Trans05	-0.131	0.0
macrophage_unactivated	0.0	-0.436
IL1	-0.409	-0.409
Rapamycin	-0.424	-0.424
Tcell	-0.45	-0.45
GMCSF	-0.364	-0.364
IFNab	-0.417	0.729
IFNg	-0.369	0.644
IFNg_GMCSF1	0.0	-0.434
Rv1432_day32	0.0	0.0
Rv1565c_day32	1.21	-0.766
secA2_input	-0.534	-0.216
delta_Rv3594	-0.197	-0.369
delta_Rv3717	0.535	0.955
delta_Rv3811	0.391	0.697
delta_Rv0954	-1.239	-0.149
PonA1	-0.773	-0.278
EccD1_KO	-1.694	-3.667
EspI_KO	-1.469	-2.264
PE35_KO	-1.502	-2.917
PPE68_KO	-1.03	-1.213
glycerol2	0.0	0.0
lignocerate	0.0	0.0
oleate	0.0	0.0
phosphatidylcholine	0.0	0.0
acetate	0.0	0.0
glucAc	0.0	0.0
Rv0950ko	-0.582	0.0
Rv1096ko	-1.252	0.0
Rv3684ko	1.716	1.14
delta_otsA_trehalose	-0.214	0.0