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 Rv2863/vapC23:

update plot	correlation	link to info on gene
Rv3098c/-	(cc=0.4702)	info on Rv3098c/-
Rv1765A/-	(cc=0.4597)	info on Rv1765A/-
Rv0302/-	(cc=0.4487)	info on Rv0302/-
Rv0309/-	(cc=0.445)	info on Rv0309/-
Rv0520/-	(cc=0.4112)	info on Rv0520/-
Rv3770B/-	(cc=0.3912)	info on Rv3770B/-
Rv2276/cyp121	(cc=0.3909)	info on Rv2276/cyp121
Rv3157/nuoM	(cc=0.3904)	info on Rv3157/nuoM
Rv0033/acpA	(cc=0.3901)	info on Rv0033/acpA
Rv2243/fabD	(cc=0.3896)	info on Rv2243/fabD

Correlation of Rv2863/vapC23 with Rv1765A/-

Normalized LFCs for Rv2863/vapC23:
(description and provenance of datasets)

	Rv2863/vapC23	Rv1765A/-
Fe_supp_jason_reseq	0.178	-0.44
low_pH_jason_reseq	-1.389	-0.599
NO_jason_reseq	-0.431	-0.042
B6_jason_reseq	-0.351	0.274
MHCII_jason_reseq	-0.883	-0.993
Isoniazid02	0.378	1.425
Rifampicin4	-0.826	-1.641
Ethambutol3	-0.528	-0.392
Meropenem3	1.095	-0.155
Vancomycin16	-0.302	0.0
Rv2680_day32	-0.091	0.754
H37Rv_KO_MarP	-0.439	-0.6
hypoxia_3wks	0.191	-0.475
hypoxia_6wks	0.121	0.146
glycerol	0.828	0.961
cholesterol	-0.171	0.282
AJ	-0.679	-2.398
Bibs02	0.955	0.886
Bibs02c	1.064	1.652
BL6	0.54	1.184
BL6a	1.002	2.309
BXD01	0.684	0.405
BXD010	0.307	1.696
BXD011	0.711	1.06
BXD03	0.813	0.407
BXD04	1.224	0.854
BXD05	-0.019	1.129
BXD06	0.995	0.26
BXD07	0.019	1.11
BXD08	1.319	0.317
BXD09	0.793	1.475
CAST	0.215	-0.712
CCcont	0.401	1.225
DS01	0.022	0.298
DS02	0.109	-1.757
DS04	2.049	-1.255
DS0c	0.275	0.995
GP01	0.85	0.136
GP02	-0.826	-1.558
GP0c	0.44	-0.334
NOD	0.0	-0.578
NZO	0.036	-2.373
PWK	1.38	-1.763
H37Rv_KO_CtpC	-0.141	-1.011
H37Rv_KO_CtpD	0.359	-0.819
H37Rv_KO_Rv1272	0.241	2.705
H37Rv_KO_SugABC	-0.659	-1.855
H37Rv_KO_MbtN	-0.137	-1.363
Trans05	1.856	0.366
macrophage_unactivated	-0.243	-0.701
IL1	-0.306	0.65
Rapamycin	-0.123	-0.341
Tcell	-0.283	-0.336
GMCSF	-0.433	-0.681
IFNab	-0.218	0.181
IFNg	-0.08	-0.917
IFNg_GMCSF1	-0.226	0.0
Rv1432_day32	1.158	1.068
Rv1565c_day32	0.957	-0.226
secA2_input	-0.787	-2.049
delta_Rv3594	-0.849	-1.885
delta_Rv3717	-0.029	-1.47
delta_Rv3811	-0.274	-1.737
delta_Rv0954	0.339	-0.3
PonA1	-0.182	-1.422
EccD1_KO	0.092	2.845
EspI_KO	0.83	1.309
PE35_KO	1.222	1.286
PPE68_KO	0.905	1.587
glycerol2	0.72	1.424
lignocerate	0.963	2.435
oleate	0.233	-2.115
phosphatidylcholine	0.746	1.931
acetate	0.705	2.229
glucAc	0.464	2.269
Rv0950ko	0.684	-0.103
Rv1096ko	1.285	0.449
Rv3684ko	0.36	1.333
delta_otsA_trehalose	0.031	-0.939