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 Rv1164/narI:

update plot	correlation	link to info on gene
Rv0333/-	(cc=0.5361)	info on Rv0333/-
Rv1482c/-	(cc=0.5358)	info on Rv1482c/-
Rv1215c/-	(cc=0.4841)	info on Rv1215c/-
Rv2504c/scoA	(cc=0.4741)	info on Rv2504c/scoA
Rv0671/lpqP	(cc=0.4612)	info on Rv0671/lpqP
Rv0418/lpqL	(cc=0.4505)	info on Rv0418/lpqL
Rv2643/arsC	(cc=0.4447)	info on Rv2643/arsC
Rv3310/sapM	(cc=0.4414)	info on Rv3310/sapM
Rv2389c/rpfD	(cc=0.4373)	info on Rv2389c/rpfD
Rv3238c/-	(cc=0.4321)	info on Rv3238c/-

Correlation of Rv1164/narI with Rv3238c/-

Normalized LFCs for Rv1164/narI:
(description and provenance of datasets)

	Rv1164/narI	Rv3238c/-
Fe_supp_jason_reseq	0.366	-0.284
low_pH_jason_reseq	-0.547	-1.181
NO_jason_reseq	0.105	-0.412
B6_jason_reseq	-1.121	-0.232
MHCII_jason_reseq	-0.146	0.04
Isoniazid02	-0.154	0.583
Rifampicin4	-0.087	0.412
Ethambutol3	1.415	1.198
Meropenem3	3.012	0.873
Vancomycin16	-0.106	0.09
Rv2680_day32	0.145	-0.093
H37Rv_KO_MarP	0.588	0.426
hypoxia_3wks	0.502	-0.227
hypoxia_6wks	0.111	0.019
glycerol	-0.633	-0.834
cholesterol	-0.141	-0.074
AJ	0.879	0.282
Bibs02	0.281	-0.57
Bibs02c	-0.056	0.441
BL6	-0.306	-0.079
BL6a	0.382	0.184
BXD01	-0.297	0.159
BXD010	0.261	-0.315
BXD011	0.144	0.0
BXD03	-0.275	0.249
BXD04	-0.492	0.702
BXD05	0.282	-0.225
BXD06	-0.101	0.249
BXD07	0.097	0.174
BXD08	0.369	-0.2
BXD09	0.116	-0.041
CAST	0.0	0.082
CCcont	-0.188	0.031
DS01	-0.096	0.14
DS02	-0.34	0.307
DS04	0.406	0.72
DS0c	0.085	0.399
GP01	0.591	0.234
GP02	0.459	0.51
GP0c	-0.635	-0.267
NOD	-0.138	0.519
NZO	-0.179	-0.202
PWK	-0.162	0.59
H37Rv_KO_CtpC	1.16	0.781
H37Rv_KO_CtpD	0.05	-0.056
H37Rv_KO_Rv1272	0.028	0.424
H37Rv_KO_SugABC	1.027	0.385
H37Rv_KO_MbtN	-0.085	0.479
Trans05	-0.108	0.706
macrophage_unactivated	-0.025	0.259
IL1	-0.113	0.033
Rapamycin	0.442	0.0
Tcell	-0.388	0.055
GMCSF	0.811	0.576
IFNab	0.435	0.148
IFNg	0.633	0.807
IFNg_GMCSF1	-0.27	0.437
Rv1432_day32	-0.017	-0.137
Rv1565c_day32	0.477	-0.141
secA2_input	-0.225	-0.507
delta_Rv3594	-1.014	0.401
delta_Rv3717	-1.274	-0.059
delta_Rv3811	-1.06	-0.15
delta_Rv0954	-0.337	0.243
PonA1	-1.005	-0.34
EccD1_KO	0.855	0.316
EspI_KO	0.568	1.212
PE35_KO	0.373	1.03
PPE68_KO	0.589	1.088
glycerol2	-0.035	0.502
lignocerate	0.086	0.514
oleate	0.542	0.625
phosphatidylcholine	0.266	0.501
acetate	-0.241	0.105
glucAc	-0.187	0.016
Rv0950ko	0.163	0.289
Rv1096ko	0.299	-0.166
Rv3684ko	-0.635	0.727
delta_otsA_trehalose	-0.57	-0.38