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 Rv3670/ephE:

update plot	correlation	link to info on gene
Rv2678c/hemE	(cc=0.7004)	info on Rv2678c/hemE
Rv0637/hadC	(cc=0.6912)	info on Rv0637/hadC
Rv3753c/-	(cc=0.6718)	info on Rv3753c/-
Rv3673c/-	(cc=0.6695)	info on Rv3673c/-
Rv3789/-	(cc=0.6629)	info on Rv3789/-
Rv2882c/frr	(cc=0.651)	info on Rv2882c/frr
Rv0701/rplC	(cc=0.6254)	info on Rv0701/rplC
Rv3258c/-	(cc=0.6211)	info on Rv3258c/-
Rv2164c/-	(cc=0.6159)	info on Rv2164c/-
Rv2968c/-	(cc=0.5958)	info on Rv2968c/-

Correlation of Rv3670/ephE with Rv3753c/-

Normalized LFCs for Rv3670/ephE:
(description and provenance of datasets)

	Rv3670/ephE	Rv3753c/-
Fe_supp_jason_reseq	1.209	1.778
low_pH_jason_reseq	0.0	0.582
NO_jason_reseq	0.362	-0.362
B6_jason_reseq	0.0	-0.153
MHCII_jason_reseq	0.0	0.0
Isoniazid02	0.0	0.0
Rifampicin4	0.0	0.0
Ethambutol3	0.0	0.0
Meropenem3	0.0	0.0
Vancomycin16	0.0	0.0
Rv2680_day32	-1.357	0.0
H37Rv_KO_MarP	-2.095	-0.255
hypoxia_3wks	0.0	0.0
hypoxia_6wks	0.0	0.0
glycerol	0.0	0.0
cholesterol	0.0	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	0.243
BXD03	0.0	0.0
BXD04	0.0	1.619
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	0.149	0.0
DS01	0.0	0.0
DS02	0.0	0.0
DS04	0.953	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	0.127
H37Rv_KO_Rv1272	0.0	0.0
H37Rv_KO_SugABC	0.348	0.0
H37Rv_KO_MbtN	0.283	0.0
Trans05	0.0	0.0
macrophage_unactivated	0.0	-0.436
IL1	0.0	-0.409
Rapamycin	0.0	-0.424
Tcell	0.0	-0.45
GMCSF	0.0	-0.364
IFNab	0.0	0.729
IFNg	0.0	0.644
IFNg_GMCSF1	0.0	-0.434
Rv1432_day32	0.0	0.0
Rv1565c_day32	0.0	-0.766
secA2_input	-0.216	-0.216
delta_Rv3594	0.266	-0.369
delta_Rv3717	1.669	0.955
delta_Rv3811	0.126	0.697
delta_Rv0954	-4.534	-0.149
PonA1	-0.866	-0.278
EccD1_KO	-2.355	-3.667
EspI_KO	-4.894	-2.264
PE35_KO	-3.949	-2.917
PPE68_KO	-3.404	-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	1.049	0.0
Rv1096ko	0.727	0.0
Rv3684ko	2.325	1.14
delta_otsA_trehalose	-1.743	0.0