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 Rv2968c/-

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

	Rv3670/ephE	Rv2968c/-
Fe_supp_jason_reseq	1.209	0.0
low_pH_jason_reseq	0.0	0.0
NO_jason_reseq	0.362	0.0
B6_jason_reseq	0.0	0.0
MHCII_jason_reseq	0.0	0.572
Isoniazid02	0.0	-1.027
Rifampicin4	0.0	1.278
Ethambutol3	0.0	0.109
Meropenem3	0.0	0.055
Vancomycin16	0.0	2.263
Rv2680_day32	-1.357	0.0
H37Rv_KO_MarP	-2.095	-2.11
hypoxia_3wks	0.0	0.0
hypoxia_6wks	0.0	0.263
glycerol	0.0	0.0
cholesterol	0.0	0.509
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	0.64
BXD010	0.0	0.0
BXD011	0.0	0.127
BXD03	0.0	0.371
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	0.149	1.002
DS01	0.0	0.236
DS02	0.0	0.0
DS04	0.953	0.194
DS0c	0.0	0.0
GP01	0.0	0.715
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	0.446
H37Rv_KO_CtpD	0.0	0.0
H37Rv_KO_Rv1272	0.0	0.0
H37Rv_KO_SugABC	0.348	1.102
H37Rv_KO_MbtN	0.283	0.0
Trans05	0.0	0.249
macrophage_unactivated	0.0	-0.436
IL1	0.0	-0.409
Rapamycin	0.0	0.0
Tcell	0.0	0.411
GMCSF	0.0	-0.364
IFNab	0.0	-0.417
IFNg	0.0	-0.369
IFNg_GMCSF1	0.0	-0.434
Rv1432_day32	0.0	0.0
Rv1565c_day32	0.0	0.0
secA2_input	-0.216	-0.116
delta_Rv3594	0.266	-0.471
delta_Rv3717	1.669	-0.771
delta_Rv3811	0.126	-1.181
delta_Rv0954	-4.534	-1.782
PonA1	-0.866	-1.287
EccD1_KO	-2.355	-1.51
EspI_KO	-4.894	-2.493
PE35_KO	-3.949	-1.613
PPE68_KO	-3.404	-0.928
glycerol2	0.0	-0.531
lignocerate	0.0	-0.462
oleate	0.0	-0.537
phosphatidylcholine	0.0	-0.531
acetate	0.0	1.15
glucAc	0.0	0.915
Rv0950ko	1.049	0.0
Rv1096ko	0.727	0.832
Rv3684ko	2.325	0.0
delta_otsA_trehalose	-1.743	0.164