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 Rv1920/-:

update plot	correlation	link to info on gene
Rv1871c/-	(cc=0.5532)	info on Rv1871c/-
Rv1800/PPE28	(cc=0.4866)	info on Rv1800/PPE28
Rv1850/ureC	(cc=0.4828)	info on Rv1850/ureC
Rv0845/-	(cc=0.4632)	info on Rv0845/-
Rv2778c/-	(cc=0.4519)	info on Rv2778c/-
Rv2435c/-	(cc=0.448)	info on Rv2435c/-
Rv0867c/rpfA	(cc=0.4344)	info on Rv0867c/rpfA
Rv2274c/mazF8	(cc=0.424)	info on Rv2274c/mazF8
Rv2584c/apt	(cc=0.4226)	info on Rv2584c/apt
Rv2038c/-	(cc=0.4208)	info on Rv2038c/-

Correlation of Rv1920/- with Rv1800/PPE28

Normalized LFCs for Rv1920/-:
(description and provenance of datasets)

	Rv1920/-	Rv1800/PPE28
Fe_supp_jason_reseq	-1.601	-0.786
low_pH_jason_reseq	-0.201	-0.224
NO_jason_reseq	-0.383	-0.123
B6_jason_reseq	-0.487	-0.969
MHCII_jason_reseq	-1.332	-0.668
Isoniazid02	-0.061	0.907
Rifampicin4	0.217	0.162
Ethambutol3	-0.094	1.313
Meropenem3	0.294	0.637
Vancomycin16	-0.093	0.263
Rv2680_day32	-0.545	-1.145
H37Rv_KO_MarP	-0.207	-0.168
hypoxia_3wks	0.658	-0.199
hypoxia_6wks	0.791	0.157
glycerol	-0.581	-0.532
cholesterol	-0.301	-0.159
AJ	0.687	0.358
Bibs02	0.062	0.282
Bibs02c	-0.174	0.244
BL6	-0.135	0.146
BL6a	0.276	-0.126
BXD01	-0.271	-0.096
BXD010	0.139	0.111
BXD011	0.064	0.618
BXD03	-0.096	-0.441
BXD04	-0.014	0.069
BXD05	0.06	-0.199
BXD06	0.102	-0.273
BXD07	0.331	-0.02
BXD08	0.123	-0.032
BXD09	0.216	-0.192
CAST	0.202	0.189
CCcont	-0.487	-0.043
DS01	0.169	-0.286
DS02	-0.194	-0.095
DS04	-0.298	0.291
DS0c	-0.063	-0.308
GP01	1.29	0.845
GP02	-0.999	0.832
GP0c	-0.62	0.124
NOD	-0.628	0.052
NZO	0.988	0.308
PWK	-0.594	0.303
H37Rv_KO_CtpC	0.241	0.486
H37Rv_KO_CtpD	0.851	0.415
H37Rv_KO_Rv1272	1.096	0.684
H37Rv_KO_SugABC	-0.058	0.616
H37Rv_KO_MbtN	0.832	0.574
Trans05	0.825	0.768
macrophage_unactivated	1.146	0.436
IL1	-0.021	0.0
Rapamycin	0.043	-0.049
Tcell	-0.3	0.153
GMCSF	1.001	0.227
IFNab	0.396	0.097
IFNg	0.925	0.107
IFNg_GMCSF1	0.393	0.148
Rv1432_day32	0.267	0.095
Rv1565c_day32	0.438	0.068
secA2_input	-1.273	-0.895
delta_Rv3594	-0.035	0.716
delta_Rv3717	0.216	-0.042
delta_Rv3811	0.0	0.223
delta_Rv0954	-0.801	0.327
PonA1	-0.298	0.089
EccD1_KO	-0.418	-0.303
EspI_KO	-0.168	-0.208
PE35_KO	-0.128	0.58
PPE68_KO	0.643	0.435
glycerol2	0.377	0.695
lignocerate	0.188	0.631
oleate	0.302	0.503
phosphatidylcholine	0.751	0.748
acetate	-0.048	0.0
glucAc	-0.178	0.268
Rv0950ko	-1.279	0.087
Rv1096ko	-1.224	-0.356
Rv3684ko	-1.035	-0.37
delta_otsA_trehalose	1.142	0.132