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 Rv3885c/eccE2

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

	Rv3699/-	Rv3885c/eccE2
Fe_supp_jason_reseq	0.339	0.44
low_pH_jason_reseq	-0.085	-0.385
NO_jason_reseq	-1.047	-0.533
B6_jason_reseq	0.316	-0.165
MHCII_jason_reseq	0.196	0.452
Isoniazid02	0.697	0.063
Rifampicin4	-0.041	-0.079
Ethambutol3	0.169	0.102
Meropenem3	0.303	0.678
Vancomycin16	0.297	0.114
Rv2680_day32	0.494	0.511
H37Rv_KO_MarP	0.188	0.243
hypoxia_3wks	-0.084	0.0
hypoxia_6wks	-0.679	0.487
glycerol	-0.925	0.462
cholesterol	-0.247	-0.15
AJ	-0.247	0.133
Bibs02	-0.021	0.787
Bibs02c	1.088	0.844
BL6	0.607	1.101
BL6a	1.045	1.492
BXD01	0.058	0.643
BXD010	0.385	0.568
BXD011	0.446	1.032
BXD03	1.211	1.332
BXD04	0.157	0.432
BXD05	0.555	0.935
BXD06	0.259	1.031
BXD07	0.404	1.253
BXD08	-0.125	0.896
BXD09	0.435	1.072
CAST	-0.454	-0.289
CCcont	0.797	1.222
DS01	0.546	0.986
DS02	0.83	0.993
DS04	-1.258	-0.159
DS0c	0.633	1.226
GP01	0.095	0.655
GP02	0.835	1.569
GP0c	0.19	0.559
NOD	-0.324	-0.547
NZO	-0.068	-0.295
PWK	-0.496	1.04
H37Rv_KO_CtpC	0.222	1.193
H37Rv_KO_CtpD	-0.028	1.848
H37Rv_KO_Rv1272	0.705	0.98
H37Rv_KO_SugABC	0.706	1.39
H37Rv_KO_MbtN	-0.508	-0.544
Trans05	0.578	-0.135
macrophage_unactivated	0.066	-0.224
IL1	-0.35	0.0
Rapamycin	-0.224	-0.129
Tcell	-0.945	0.046
GMCSF	-0.523	0.512
IFNab	0.29	0.438
IFNg	-0.508	0.144
IFNg_GMCSF1	0.742	0.0
Rv1432_day32	0.673	0.525
Rv1565c_day32	-0.09	0.126
secA2_input	-0.473	-0.56
delta_Rv3594	0.236	-0.823
delta_Rv3717	-0.495	-0.836
delta_Rv3811	0.07	-0.629
delta_Rv0954	-0.508	-0.506
PonA1	-0.237	-0.157
EccD1_KO	0.355	0.585
EspI_KO	0.57	0.143
PE35_KO	0.933	-0.265
PPE68_KO	1.075	0.118
glycerol2	-0.128	0.345
lignocerate	-0.061	0.257
oleate	0.095	0.058
phosphatidylcholine	-0.325	0.14
acetate	0.201	-0.178
glucAc	-0.115	-0.111
Rv0950ko	0.286	-0.362
Rv1096ko	0.579	0.087
Rv3684ko	0.95	0.187
delta_otsA_trehalose	0.546	0.833