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 Rv3539/PPE63:

update plot	correlation	link to info on gene
Rv3713/cobQ2	(cc=0.5056)	info on Rv3713/cobQ2
Rv0552/-	(cc=0.4871)	info on Rv0552/-
Rv0273c/-	(cc=0.4803)	info on Rv0273c/-
Rv0687/-	(cc=0.4759)	info on Rv0687/-
Rv2164c/-	(cc=0.4629)	info on Rv2164c/-
Rv2678c/hemE	(cc=0.4562)	info on Rv2678c/hemE
Rv0144/-	(cc=0.4502)	info on Rv0144/-
Rv0701/rplC	(cc=0.4445)	info on Rv0701/rplC
Rv1339/-	(cc=0.4403)	info on Rv1339/-
Rv1191/-	(cc=0.4401)	info on Rv1191/-

Correlation of Rv3539/PPE63 with Rv0552/-

Normalized LFCs for Rv3539/PPE63:
(description and provenance of datasets)

	Rv3539/PPE63	Rv0552/-
Fe_supp_jason_reseq	-0.025	-0.33
low_pH_jason_reseq	0.867	2.951
NO_jason_reseq	0.407	0.449
B6_jason_reseq	-0.193	0.71
MHCII_jason_reseq	-0.049	1.279
Isoniazid02	0.07	-0.064
Rifampicin4	0.612	0.079
Ethambutol3	-0.255	-0.327
Meropenem3	2.53	1.355
Vancomycin16	0.544	0.26
Rv2680_day32	-0.683	-0.532
H37Rv_KO_MarP	0.337	0.363
hypoxia_3wks	0.347	0.144
hypoxia_6wks	0.986	0.424
glycerol	-0.225	0.054
cholesterol	-0.162	0.329
AJ	0.395	0.724
Bibs02	1.08	0.128
Bibs02c	0.471	0.694
BL6	-0.338	0.066
BL6a	0.247	-0.019
BXD01	0.348	0.277
BXD010	-0.07	0.101
BXD011	0.545	-0.199
BXD03	-0.389	-0.212
BXD04	0.529	0.033
BXD05	0.516	-0.476
BXD06	-0.13	0.37
BXD07	-0.018	-0.247
BXD08	0.052	0.705
BXD09	0.108	-0.106
CAST	0.177	0.35
CCcont	-0.188	-0.041
DS01	-0.481	0.145
DS02	-0.058	-0.206
DS04	-0.188	-0.223
DS0c	0.218	-0.121
GP01	0.423	0.203
GP02	1.274	0.177
GP0c	0.728	-0.477
NOD	0.254	0.639
NZO	0.906	1.024
PWK	0.173	0.612
H37Rv_KO_CtpC	0.467	0.234
H37Rv_KO_CtpD	0.629	0.563
H37Rv_KO_Rv1272	1.146	-0.48
H37Rv_KO_SugABC	0.858	0.225
H37Rv_KO_MbtN	0.494	-0.088
Trans05	0.782	0.209
macrophage_unactivated	-0.211	0.17
IL1	-0.409	-0.519
Rapamycin	0.132	-0.215
Tcell	-0.143	0.0
GMCSF	-0.301	0.51
IFNab	0.067	-0.085
IFNg	-0.633	-0.037
IFNg_GMCSF1	0.201	-0.044
Rv1432_day32	0.026	0.068
Rv1565c_day32	1.005	0.521
secA2_input	0.661	-0.456
delta_Rv3594	0.684	1.078
delta_Rv3717	1.031	0.876
delta_Rv3811	0.805	0.0
delta_Rv0954	0.0	-0.332
PonA1	0.744	0.711
EccD1_KO	-0.997	-0.21
EspI_KO	-0.642	-0.488
PE35_KO	-0.977	-1.164
PPE68_KO	-1.177	-1.021
glycerol2	-0.092	-0.422
lignocerate	0.188	-0.317
oleate	0.197	-0.111
phosphatidylcholine	0.132	-0.013
acetate	-0.791	-0.535
glucAc	-0.068	-0.583
Rv0950ko	0.0	0.051
Rv1096ko	0.368	1.487
Rv3684ko	0.0	0.714
delta_otsA_trehalose	-0.075	-0.461