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 Rv0302/-

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

	Rv2863/vapC23	Rv0302/-
Fe_supp_jason_reseq	0.178	-0.903
low_pH_jason_reseq	-1.389	-0.549
NO_jason_reseq	-0.431	-0.079
B6_jason_reseq	-0.351	-0.488
MHCII_jason_reseq	-0.883	0.451
Isoniazid02	0.378	0.287
Rifampicin4	-0.826	-0.639
Ethambutol3	-0.528	-0.382
Meropenem3	1.095	-0.007
Vancomycin16	-0.302	0.101
Rv2680_day32	-0.091	-0.199
H37Rv_KO_MarP	-0.439	0.288
hypoxia_3wks	0.191	-0.431
hypoxia_6wks	0.121	0.257
glycerol	0.828	0.332
cholesterol	-0.171	0.022
AJ	-0.679	0.343
Bibs02	0.955	0.513
Bibs02c	1.064	0.876
BL6	0.54	-0.038
BL6a	1.002	0.456
BXD01	0.684	-0.045
BXD010	0.307	-0.279
BXD011	0.711	0.415
BXD03	0.813	0.665
BXD04	1.224	-0.165
BXD05	-0.019	-0.293
BXD06	0.995	0.02
BXD07	0.019	0.051
BXD08	1.319	-0.093
BXD09	0.793	-0.152
CAST	0.215	-0.267
CCcont	0.401	0.414
DS01	0.022	0.017
DS02	0.109	0.722
DS04	2.049	0.299
DS0c	0.275	0.677
GP01	0.85	-0.277
GP02	-0.826	-1.403
GP0c	0.44	-0.296
NOD	0.0	-0.939
NZO	0.036	-0.231
PWK	1.38	-0.392
H37Rv_KO_CtpC	-0.141	-0.095
H37Rv_KO_CtpD	0.359	0.606
H37Rv_KO_Rv1272	0.241	0.444
H37Rv_KO_SugABC	-0.659	-1.377
H37Rv_KO_MbtN	-0.137	-0.778
Trans05	1.856	0.005
macrophage_unactivated	-0.243	-0.679
IL1	-0.306	-0.377
Rapamycin	-0.123	-1.022
Tcell	-0.283	-0.179
GMCSF	-0.433	0.063
IFNab	-0.218	-0.55
IFNg	-0.08	-0.16
IFNg_GMCSF1	-0.226	-0.657
Rv1432_day32	1.158	0.694
Rv1565c_day32	0.957	-0.114
secA2_input	-0.787	0.495
delta_Rv3594	-0.849	-1.358
delta_Rv3717	-0.029	-1.286
delta_Rv3811	-0.274	-1.93
delta_Rv0954	0.339	-0.933
PonA1	-0.182	-1.113
EccD1_KO	0.092	-0.217
EspI_KO	0.83	0.0
PE35_KO	1.222	0.184
PPE68_KO	0.905	0.256
glycerol2	0.72	0.894
lignocerate	0.963	1.447
oleate	0.233	-0.343
phosphatidylcholine	0.746	0.805
acetate	0.705	0.579
glucAc	0.464	0.801
Rv0950ko	0.684	0.706
Rv1096ko	1.285	0.187
Rv3684ko	0.36	0.069
delta_otsA_trehalose	0.031	0.148