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 Rv2252/-:

update plot	correlation	link to info on gene
Rv0697/-	(cc=0.4786)	info on Rv0697/-
Rv2403c/lppR	(cc=0.4473)	info on Rv2403c/lppR
Rv2620c/-	(cc=0.392)	info on Rv2620c/-
Rv3069/-	(cc=0.3882)	info on Rv3069/-
Rv2740/ephG	(cc=0.3881)	info on Rv2740/ephG
Rv3215/entC	(cc=0.3845)	info on Rv3215/entC
Rv2455c/-	(cc=0.3739)	info on Rv2455c/-
Rv2454c/-	(cc=0.3708)	info on Rv2454c/-
Rv2461c/clpP1	(cc=0.3563)	info on Rv2461c/clpP1
Rv2043c/pncA	(cc=0.3563)	info on Rv2043c/pncA

Correlation of Rv2252/- with Rv2454c/-

Normalized LFCs for Rv2252/-:
(description and provenance of datasets)

	Rv2252/-	Rv2454c/-
Fe_supp_jason_reseq	0.268	0.0
low_pH_jason_reseq	0.371	0.0
NO_jason_reseq	0.446	0.0
B6_jason_reseq	0.777	0.0
MHCII_jason_reseq	1.625	0.0
Isoniazid02	0.787	0.851
Rifampicin4	0.0	0.0
Ethambutol3	0.0	0.0
Meropenem3	-0.254	0.0
Vancomycin16	0.0	0.0
Rv2680_day32	-0.131	0.0
H37Rv_KO_MarP	-0.43	1.081
hypoxia_3wks	0.12	0.0
hypoxia_6wks	0.063	0.0
glycerol	0.0	0.0
cholesterol	-0.159	0.0
AJ	-0.541	0.0
Bibs02	0.502	0.0
Bibs02c	-0.23	0.0
BL6	0.217	0.0
BL6a	0.377	0.0
BXD01	0.054	0.0
BXD010	-1.039	0.0
BXD011	1.085	0.0
BXD03	-0.214	0.0
BXD04	0.051	0.0
BXD05	0.302	0.0
BXD06	-0.211	0.0
BXD07	0.38	0.0
BXD08	-0.177	0.0
BXD09	-0.091	0.0
CAST	-0.661	0.0
CCcont	-0.199	0.0
DS01	-0.315	0.0
DS02	0.377	0.0
DS04	-0.453	0.0
DS0c	-1.397	0.0
GP01	0.021	0.099
GP02	1.364	0.0
GP0c	-0.337	0.0
NOD	-1.279	0.0
NZO	0.448	0.0
PWK	-1.117	0.0
H37Rv_KO_CtpC	-0.758	0.0
H37Rv_KO_CtpD	-0.027	0.445
H37Rv_KO_Rv1272	0.364	0.0
H37Rv_KO_SugABC	-1.477	0.0
H37Rv_KO_MbtN	-0.791	0.0
Trans05	-0.411	0.0
macrophage_unactivated	1.105	0.0
IL1	-0.11	0.0
Rapamycin	0.424	0.0
Tcell	0.45	0.0
GMCSF	1.545	0.0
IFNab	0.514	0.0
IFNg	1.689	0.0
IFNg_GMCSF1	1.191	0.0
Rv1432_day32	-0.445	0.0
Rv1565c_day32	0.131	0.0
secA2_input	-2.311	-2.955
delta_Rv3594	1.037	0.0
delta_Rv3717	0.331	0.0
delta_Rv3811	-0.33	0.0
delta_Rv0954	0.249	0.178
PonA1	0.691	0.159
EccD1_KO	0.997	0.0
EspI_KO	-0.588	0.0
PE35_KO	0.648	0.767
PPE68_KO	0.841	0.442
glycerol2	0.05	0.0
lignocerate	0.357	0.0
oleate	0.147	0.0
phosphatidylcholine	0.193	0.0
acetate	0.173	0.229
glucAc	0.037	0.143
Rv0950ko	0.0	-0.38
Rv1096ko	0.112	-0.793
Rv3684ko	-0.511	-0.413
delta_otsA_trehalose	0.818	-0.027