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 Rv3714c/-:

update plot	correlation	link to info on gene
Rv0233/nrdB	(cc=0.5081)	info on Rv0233/nrdB
Rv0592/mce2D	(cc=0.4955)	info on Rv0592/mce2D
Rv3733c/-	(cc=0.4877)	info on Rv3733c/-
Rv0395/-	(cc=0.469)	info on Rv0395/-
Rv2994/-	(cc=0.4678)	info on Rv2994/-
Rv2771c/-	(cc=0.4464)	info on Rv2771c/-
Rv3696c/glpK	(cc=0.4447)	info on Rv3696c/glpK
Rv1318c/-	(cc=0.4427)	info on Rv1318c/-
Rv1135A/-	(cc=0.4413)	info on Rv1135A/-
Rv0303/-	(cc=0.4338)	info on Rv0303/-

Correlation of Rv3714c/- with Rv0303/-

Normalized LFCs for Rv3714c/-:
(description and provenance of datasets)

	Rv3714c/-	Rv0303/-
Fe_supp_jason_reseq	-0.398	0.071
low_pH_jason_reseq	-0.363	-0.577
NO_jason_reseq	0.011	-0.494
B6_jason_reseq	0.719	0.857
MHCII_jason_reseq	1.035	-0.077
Isoniazid02	0.778	-0.162
Rifampicin4	-0.011	-0.13
Ethambutol3	0.55	-0.206
Meropenem3	-0.108	-0.156
Vancomycin16	1.387	-0.127
Rv2680_day32	0.488	0.829
H37Rv_KO_MarP	0.169	0.241
hypoxia_3wks	0.49	0.136
hypoxia_6wks	1.184	0.66
glycerol	-1.508	-0.13
cholesterol	-0.909	-0.764
AJ	0.202	-0.343
Bibs02	-0.147	-0.65
Bibs02c	0.108	0.853
BL6	-0.168	0.246
BL6a	-0.013	0.098
BXD01	0.43	-0.735
BXD010	0.139	-0.357
BXD011	0.21	-0.805
BXD03	0.323	-0.487
BXD04	0.597	-0.092
BXD05	-0.14	-0.316
BXD06	0.267	-0.356
BXD07	0.08	-0.369
BXD08	0.297	-1.018
BXD09	0.279	-0.325
CAST	0.607	0.317
CCcont	-0.643	-0.969
DS01	0.433	-0.075
DS02	0.651	0.325
DS04	1.023	0.24
DS0c	0.638	0.239
GP01	-0.144	-0.658
GP02	0.641	-1.356
GP0c	-0.46	-0.727
NOD	1.111	0.436
NZO	0.526	-0.376
PWK	0.367	0.159
H37Rv_KO_CtpC	-0.288	-0.116
H37Rv_KO_CtpD	0.055	0.669
H37Rv_KO_Rv1272	-1.053	0.418
H37Rv_KO_SugABC	-0.819	-1.585
H37Rv_KO_MbtN	-0.526	-1.073
Trans05	-0.625	-0.511
macrophage_unactivated	0.095	-0.177
IL1	0.0	-0.092
Rapamycin	-0.19	-0.733
Tcell	0.935	-0.287
GMCSF	0.079	-0.301
IFNab	-0.333	-0.856
IFNg	-0.029	-0.083
IFNg_GMCSF1	-0.072	-0.984
Rv1432_day32	1.288	0.31
Rv1565c_day32	0.158	0.028
secA2_input	0.769	0.554
delta_Rv3594	-0.971	-0.58
delta_Rv3717	-0.799	-0.312
delta_Rv3811	-1.387	-0.739
delta_Rv0954	-1.0	-0.868
PonA1	-0.336	-0.119
EccD1_KO	-0.697	-0.197
EspI_KO	-0.371	-0.836
PE35_KO	-0.446	-0.744
PPE68_KO	-0.403	-0.733
glycerol2	-0.661	-0.067
lignocerate	-0.621	-0.311
oleate	-0.793	0.024
phosphatidylcholine	-0.793	-0.126
acetate	-1.614	-0.603
glucAc	-0.741	-0.315
Rv0950ko	0.724	0.651
Rv1096ko	0.552	1.095
Rv3684ko	0.196	0.956
delta_otsA_trehalose	0.411	1.464