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 Rv3490/otsA:

update plot	correlation	link to info on gene
Rv3603c/-	(cc=0.7602)	info on Rv3603c/-
Rv2399c/cysT	(cc=0.7456)	info on Rv2399c/cysT
Rv3588c/canB	(cc=0.7206)	info on Rv3588c/canB
Rv2397c/cysA1	(cc=0.699)	info on Rv2397c/cysA1
Rv1285/cysD	(cc=0.6637)	info on Rv1285/cysD
Rv1324/-	(cc=0.6271)	info on Rv1324/-
Rv0467/icl1	(cc=0.6248)	info on Rv0467/icl1
Rv3035/-	(cc=0.5969)	info on Rv3035/-
Rv2115c/mpa	(cc=0.5883)	info on Rv2115c/mpa
Rv2844/-	(cc=0.5819)	info on Rv2844/-

Correlation of Rv3490/otsA with Rv3603c/-

Normalized LFCs for Rv3490/otsA:
(description and provenance of datasets)

	Rv3490/otsA	Rv3603c/-
Fe_supp_jason_reseq	0.0	0.0
low_pH_jason_reseq	0.0	0.0
NO_jason_reseq	0.0	0.0
B6_jason_reseq	0.0	0.0
MHCII_jason_reseq	0.0	0.0
Isoniazid02	-0.383	0.0
Rifampicin4	0.601	0.0
Ethambutol3	0.14	0.0
Meropenem3	-0.151	0.0
Vancomycin16	1.101	0.0
Rv2680_day32	0.0	0.0
H37Rv_KO_MarP	-0.151	-1.081
hypoxia_3wks	0.0	0.0
hypoxia_6wks	0.0	0.0
glycerol	0.202	0.0
cholesterol	0.276	0.0
AJ	0.0	0.0
Bibs02	0.0	0.0
Bibs02c	0.0	0.0
BL6	0.0	0.0
BL6a	0.0	0.0
BXD01	0.0	0.0
BXD010	0.0	0.0
BXD011	0.0	0.0
BXD03	0.0	0.0
BXD04	0.0	0.0
BXD05	0.0	0.0
BXD06	0.0	0.0
BXD07	0.0	0.0
BXD08	0.0	0.0
BXD09	0.0	0.0
CAST	0.0	0.0
CCcont	0.285	0.0
DS01	0.0	0.0
DS02	0.0	0.0
DS04	0.0	0.0
DS0c	0.0	0.0
GP01	0.0	0.0
GP02	0.0	0.0
GP0c	0.0	0.0
NOD	0.0	0.0
NZO	0.0	0.0
PWK	0.0	0.0
H37Rv_KO_CtpC	0.0	0.0
H37Rv_KO_CtpD	0.0	0.0
H37Rv_KO_Rv1272	0.0	0.0
H37Rv_KO_SugABC	0.0	0.0
H37Rv_KO_MbtN	0.0	0.0
Trans05	0.0	0.0
macrophage_unactivated	0.0	0.0
IL1	0.0	0.0
Rapamycin	0.0	0.0
Tcell	0.0	0.0
GMCSF	0.0	0.0
IFNab	0.0	0.0
IFNg	0.0	0.0
IFNg_GMCSF1	0.0	0.0
Rv1432_day32	0.0	0.0
Rv1565c_day32	0.0	0.0
secA2_input	-0.916	-1.061
delta_Rv3594	0.0	0.0
delta_Rv3717	0.0	0.0
delta_Rv3811	0.0	0.0
delta_Rv0954	0.0	0.178
PonA1	0.0	0.0
EccD1_KO	-1.145	0.0
EspI_KO	0.55	0.0
PE35_KO	1.706	2.473
PPE68_KO	0.896	1.872
glycerol2	0.0	0.0
lignocerate	0.0	0.0
oleate	0.0	0.0
phosphatidylcholine	0.0	0.0
acetate	0.229	0.0
glucAc	0.392	0.0
Rv0950ko	-0.844	-0.28
Rv1096ko	-1.517	-1.632
Rv3684ko	-0.917	-0.632
delta_otsA_trehalose	0.0	0.133