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 Rv0520/-

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

	Rv2863/vapC23	Rv0520/-
Fe_supp_jason_reseq	0.178	0.208
low_pH_jason_reseq	-1.389	-1.092
NO_jason_reseq	-0.431	0.2
B6_jason_reseq	-0.351	0.285
MHCII_jason_reseq	-0.883	-0.78
Isoniazid02	0.378	0.457
Rifampicin4	-0.826	-1.034
Ethambutol3	-0.528	0.006
Meropenem3	1.095	0.099
Vancomycin16	-0.302	0.069
Rv2680_day32	-0.091	-0.564
H37Rv_KO_MarP	-0.439	0.474
hypoxia_3wks	0.191	-0.056
hypoxia_6wks	0.121	0.443
glycerol	0.828	0.012
cholesterol	-0.171	0.132
AJ	-0.679	0.261
Bibs02	0.955	0.021
Bibs02c	1.064	-0.158
BL6	0.54	-0.439
BL6a	1.002	-0.179
BXD01	0.684	-0.289
BXD010	0.307	-0.019
BXD011	0.711	-0.328
BXD03	0.813	-0.324
BXD04	1.224	0.165
BXD05	-0.019	0.383
BXD06	0.995	-0.126
BXD07	0.019	-0.254
BXD08	1.319	-0.484
BXD09	0.793	-0.088
CAST	0.215	0.027
CCcont	0.401	-0.459
DS01	0.022	0.571
DS02	0.109	0.35
DS04	2.049	-0.086
DS0c	0.275	0.646
GP01	0.85	0.722
GP02	-0.826	-0.881
GP0c	0.44	-0.168
NOD	0.0	1.059
NZO	0.036	-0.358
PWK	1.38	0.533
H37Rv_KO_CtpC	-0.141	0.706
H37Rv_KO_CtpD	0.359	-0.755
H37Rv_KO_Rv1272	0.241	-0.308
H37Rv_KO_SugABC	-0.659	-2.11
H37Rv_KO_MbtN	-0.137	-1.846
Trans05	1.856	1.507
macrophage_unactivated	-0.243	-0.294
IL1	-0.306	-0.306
Rapamycin	-0.123	-0.114
Tcell	-0.283	-0.613
GMCSF	-0.433	0.417
IFNab	-0.218	-0.52
IFNg	-0.08	-0.543
IFNg_GMCSF1	-0.226	-0.478
Rv1432_day32	1.158	0.366
Rv1565c_day32	0.957	-0.543
secA2_input	-0.787	-0.291
delta_Rv3594	-0.849	-0.621
delta_Rv3717	-0.029	-0.257
delta_Rv3811	-0.274	0.0
delta_Rv0954	0.339	-0.426
PonA1	-0.182	-0.027
EccD1_KO	0.092	1.575
EspI_KO	0.83	1.68
PE35_KO	1.222	0.668
PPE68_KO	0.905	1.165
glycerol2	0.72	0.409
lignocerate	0.963	0.132
oleate	0.233	0.288
phosphatidylcholine	0.746	0.416
acetate	0.705	-0.204
glucAc	0.464	0.057
Rv0950ko	0.684	1.236
Rv1096ko	1.285	1.915
Rv3684ko	0.36	1.294
delta_otsA_trehalose	0.031	-0.237