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 Rv0144/-

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

	Rv3539/PPE63	Rv0144/-
Fe_supp_jason_reseq	-0.025	0.106
low_pH_jason_reseq	0.867	-0.88
NO_jason_reseq	0.407	-0.858
B6_jason_reseq	-0.193	-0.045
MHCII_jason_reseq	-0.049	0.441
Isoniazid02	0.07	-0.923
Rifampicin4	0.612	-0.217
Ethambutol3	-0.255	-0.303
Meropenem3	2.53	0.611
Vancomycin16	0.544	-0.966
Rv2680_day32	-0.683	0.026
H37Rv_KO_MarP	0.337	-0.021
hypoxia_3wks	0.347	0.179
hypoxia_6wks	0.986	0.077
glycerol	-0.225	-0.888
cholesterol	-0.162	-0.69
AJ	0.395	-0.351
Bibs02	1.08	-0.024
Bibs02c	0.471	0.526
BL6	-0.338	-0.711
BL6a	0.247	-0.148
BXD01	0.348	0.252
BXD010	-0.07	-0.398
BXD011	0.545	-0.325
BXD03	-0.389	-0.464
BXD04	0.529	0.449
BXD05	0.516	0.0
BXD06	-0.13	0.032
BXD07	-0.018	-0.339
BXD08	0.052	-0.021
BXD09	0.108	-0.133
CAST	0.177	0.384
CCcont	-0.188	-0.83
DS01	-0.481	-0.089
DS02	-0.058	0.178
DS04	-0.188	0.288
DS0c	0.218	1.087
GP01	0.423	0.784
GP02	1.274	1.281
GP0c	0.728	-0.116
NOD	0.254	-0.024
NZO	0.906	0.407
PWK	0.173	0.117
H37Rv_KO_CtpC	0.467	0.349
H37Rv_KO_CtpD	0.629	0.388
H37Rv_KO_Rv1272	1.146	0.721
H37Rv_KO_SugABC	0.858	0.593
H37Rv_KO_MbtN	0.494	-0.089
Trans05	0.782	0.154
macrophage_unactivated	-0.211	-0.543
IL1	-0.409	0.409
Rapamycin	0.132	-0.601
Tcell	-0.143	-0.042
GMCSF	-0.301	0.256
IFNab	0.067	-0.81
IFNg	-0.633	-0.23
IFNg_GMCSF1	0.201	0.163
Rv1432_day32	0.026	1.115
Rv1565c_day32	1.005	0.714
secA2_input	0.661	0.091
delta_Rv3594	0.684	-0.705
delta_Rv3717	1.031	-0.131
delta_Rv3811	0.805	-0.112
delta_Rv0954	0.0	0.154
PonA1	0.744	0.083
EccD1_KO	-0.997	-0.641
EspI_KO	-0.642	-0.93
PE35_KO	-0.977	-0.96
PPE68_KO	-1.177	-1.065
glycerol2	-0.092	-0.425
lignocerate	0.188	-0.63
oleate	0.197	0.095
phosphatidylcholine	0.132	-0.164
acetate	-0.791	-1.009
glucAc	-0.068	-1.246
Rv0950ko	0.0	0.507
Rv1096ko	0.368	0.084
Rv3684ko	0.0	0.193
delta_otsA_trehalose	-0.075	-0.144