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 Rv3699/-:

update plot	correlation	link to info on gene
Rv3232c/ppk2	(cc=0.4829)	info on Rv3232c/ppk2
Rv3885c/eccE2	(cc=0.4714)	info on Rv3885c/eccE2
Rv0786c/-	(cc=0.4527)	info on Rv0786c/-
Rv0028/-	(cc=0.4235)	info on Rv0028/-
Rv2481c/-	(cc=0.4135)	info on Rv2481c/-
Rv1116/-	(cc=0.4055)	info on Rv1116/-
Rv3143/-	(cc=0.4031)	info on Rv3143/-
Rv3071/-	(cc=0.3988)	info on Rv3071/-
Rv0915c/PPE14	(cc=0.3905)	info on Rv0915c/PPE14
Rv1665/pks11	(cc=0.385)	info on Rv1665/pks11

Correlation of Rv3699/- with Rv3232c/ppk2

Normalized LFCs for Rv3699/-:
(description and provenance of datasets)

	Rv3699/-	Rv3232c/ppk2
Fe_supp_jason_reseq	0.339	-0.068
low_pH_jason_reseq	-0.085	-1.066
NO_jason_reseq	-1.047	-1.047
B6_jason_reseq	0.316	-1.198
MHCII_jason_reseq	0.196	-1.093
Isoniazid02	0.697	0.221
Rifampicin4	-0.041	-0.233
Ethambutol3	0.169	0.328
Meropenem3	0.303	-0.364
Vancomycin16	0.297	-0.342
Rv2680_day32	0.494	0.064
H37Rv_KO_MarP	0.188	-0.037
hypoxia_3wks	-0.084	-1.435
hypoxia_6wks	-0.679	-1.128
glycerol	-0.925	-0.607
cholesterol	-0.247	-0.317
AJ	-0.247	0.56
Bibs02	-0.021	0.009
Bibs02c	1.088	0.593
BL6	0.607	0.924
BL6a	1.045	1.425
BXD01	0.058	1.132
BXD010	0.385	0.856
BXD011	0.446	0.862
BXD03	1.211	1.061
BXD04	0.157	0.856
BXD05	0.555	1.516
BXD06	0.259	1.003
BXD07	0.404	0.976
BXD08	-0.125	1.19
BXD09	0.435	1.098
CAST	-0.454	0.067
CCcont	0.797	0.915
DS01	0.546	0.407
DS02	0.83	0.31
DS04	-1.258	-0.436
DS0c	0.633	0.976
GP01	0.095	-0.087
GP02	0.835	0.119
GP0c	0.19	-0.007
NOD	-0.324	-0.244
NZO	-0.068	0.377
PWK	-0.496	-0.068
H37Rv_KO_CtpC	0.222	1.53
H37Rv_KO_CtpD	-0.028	1.154
H37Rv_KO_Rv1272	0.705	0.961
H37Rv_KO_SugABC	0.706	1.017
H37Rv_KO_MbtN	-0.508	1.109
Trans05	0.578	1.166
macrophage_unactivated	0.066	0.489
IL1	-0.35	-0.35
Rapamycin	-0.224	-0.35
Tcell	-0.945	-0.248
GMCSF	-0.523	-0.063
IFNab	0.29	0.284
IFNg	-0.508	-0.465
IFNg_GMCSF1	0.742	0.119
Rv1432_day32	0.673	0.961
Rv1565c_day32	-0.09	0.126
secA2_input	-0.473	0.111
delta_Rv3594	0.236	0.234
delta_Rv3717	-0.495	-0.279
delta_Rv3811	0.07	0.086
delta_Rv0954	-0.508	0.044
PonA1	-0.237	-0.224
EccD1_KO	0.355	0.293
EspI_KO	0.57	0.605
PE35_KO	0.933	0.443
PPE68_KO	1.075	0.272
glycerol2	-0.128	0.807
lignocerate	-0.061	0.594
oleate	0.095	0.44
phosphatidylcholine	-0.325	0.44
acetate	0.201	-0.301
glucAc	-0.115	0.131
Rv0950ko	0.286	0.235
Rv1096ko	0.579	-0.069
Rv3684ko	0.95	0.246
delta_otsA_trehalose	0.546	0.616