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 Rv2579/dhaA:

update plot	correlation	link to info on gene
Rv3238c/-	(cc=0.5305)	info on Rv3238c/-
Rv2770c/PPE44	(cc=0.4747)	info on Rv2770c/PPE44
Rv0654/-	(cc=0.4699)	info on Rv0654/-
Rv3092c/-	(cc=0.4456)	info on Rv3092c/-
Rv1862/adhA	(cc=0.4437)	info on Rv1862/adhA
Rv1844c/gnd1	(cc=0.4369)	info on Rv1844c/gnd1
Rv1915/aceAa	(cc=0.4332)	info on Rv1915/aceAa
Rv3234c/tgs3	(cc=0.4318)	info on Rv3234c/tgs3
Rv1847/-	(cc=0.4307)	info on Rv1847/-
Rv1249c/-	(cc=0.4245)	info on Rv1249c/-

Correlation of Rv2579/dhaA with Rv3238c/-

Normalized LFCs for Rv2579/dhaA:
(description and provenance of datasets)

	Rv2579/dhaA	Rv3238c/-
Fe_supp_jason_reseq	-0.407	-0.284
low_pH_jason_reseq	-0.845	-1.181
NO_jason_reseq	0.034	-0.412
B6_jason_reseq	0.28	-0.232
MHCII_jason_reseq	0.117	0.04
Isoniazid02	0.655	0.583
Rifampicin4	0.498	0.412
Ethambutol3	0.878	1.198
Meropenem3	0.079	0.873
Vancomycin16	0.196	0.09
Rv2680_day32	0.432	-0.093
H37Rv_KO_MarP	0.085	0.426
hypoxia_3wks	0.06	-0.227
hypoxia_6wks	-0.077	0.019
glycerol	-0.787	-0.834
cholesterol	-0.824	-0.074
AJ	0.657	0.282
Bibs02	-0.411	-0.57
Bibs02c	-0.138	0.441
BL6	0.853	-0.079
BL6a	-0.174	0.184
BXD01	0.0	0.159
BXD010	-0.019	-0.315
BXD011	-0.104	0.0
BXD03	0.152	0.249
BXD04	-0.286	0.702
BXD05	-0.515	-0.225
BXD06	-0.074	0.249
BXD07	-0.135	0.174
BXD08	0.251	-0.2
BXD09	-0.224	-0.041
CAST	0.185	0.082
CCcont	0.257	0.031
DS01	0.503	0.14
DS02	-0.31	0.307
DS04	0.909	0.72
DS0c	0.214	0.399
GP01	0.084	0.234
GP02	1.387	0.51
GP0c	-0.284	-0.267
NOD	0.301	0.519
NZO	0.551	-0.202
PWK	0.925	0.59
H37Rv_KO_CtpC	-0.056	0.781
H37Rv_KO_CtpD	-0.025	-0.056
H37Rv_KO_Rv1272	0.441	0.424
H37Rv_KO_SugABC	0.436	0.385
H37Rv_KO_MbtN	0.208	0.479
Trans05	-0.073	0.706
macrophage_unactivated	0.685	0.259
IL1	0.534	0.033
Rapamycin	1.062	0.0
Tcell	0.587	0.055
GMCSF	0.425	0.576
IFNab	0.311	0.148
IFNg	0.834	0.807
IFNg_GMCSF1	1.087	0.437
Rv1432_day32	0.36	-0.137
Rv1565c_day32	0.169	-0.141
secA2_input	-0.258	-0.507
delta_Rv3594	-0.038	0.401
delta_Rv3717	0.128	-0.059
delta_Rv3811	-0.086	-0.15
delta_Rv0954	0.245	0.243
PonA1	-1.099	-0.34
EccD1_KO	0.309	0.316
EspI_KO	0.222	1.212
PE35_KO	0.732	1.03
PPE68_KO	0.458	1.088
glycerol2	0.622	0.502
lignocerate	0.595	0.514
oleate	0.515	0.625
phosphatidylcholine	0.765	0.501
acetate	0.294	0.105
glucAc	0.055	0.016
Rv0950ko	0.021	0.289
Rv1096ko	0.241	-0.166
Rv3684ko	-0.046	0.727
delta_otsA_trehalose	-0.585	-0.38