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 Rv2389c/rpfD

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

	Rv1164/narI	Rv2389c/rpfD
Fe_supp_jason_reseq	0.366	-0.362
low_pH_jason_reseq	-0.547	-0.435
NO_jason_reseq	0.105	0.197
B6_jason_reseq	-1.121	-0.716
MHCII_jason_reseq	-0.146	-0.625
Isoniazid02	-0.154	0.086
Rifampicin4	-0.087	0.049
Ethambutol3	1.415	-0.016
Meropenem3	3.012	2.093
Vancomycin16	-0.106	-0.064
Rv2680_day32	0.145	0.647
H37Rv_KO_MarP	0.588	0.553
hypoxia_3wks	0.502	0.355
hypoxia_6wks	0.111	-0.019
glycerol	-0.633	0.891
cholesterol	-0.141	-0.168
AJ	0.879	0.0
Bibs02	0.281	-0.17
Bibs02c	-0.056	0.435
BL6	-0.306	0.489
BL6a	0.382	0.672
BXD01	-0.297	-0.141
BXD010	0.261	0.577
BXD011	0.144	0.542
BXD03	-0.275	0.242
BXD04	-0.492	0.34
BXD05	0.282	0.563
BXD06	-0.101	0.173
BXD07	0.097	0.135
BXD08	0.369	-0.097
BXD09	0.116	0.337
CAST	0.0	0.135
CCcont	-0.188	-0.29
DS01	-0.096	0.026
DS02	-0.34	-0.047
DS04	0.406	0.342
DS0c	0.085	-0.286
GP01	0.591	0.004
GP02	0.459	0.234
GP0c	-0.635	0.43
NOD	-0.138	0.298
NZO	-0.179	-0.176
PWK	-0.162	0.128
H37Rv_KO_CtpC	1.16	0.735
H37Rv_KO_CtpD	0.05	0.486
H37Rv_KO_Rv1272	0.028	1.233
H37Rv_KO_SugABC	1.027	0.781
H37Rv_KO_MbtN	-0.085	0.418
Trans05	-0.108	0.521
macrophage_unactivated	-0.025	0.597
IL1	-0.113	0.887
Rapamycin	0.442	1.148
Tcell	-0.388	-0.994
GMCSF	0.811	0.969
IFNab	0.435	0.865
IFNg	0.633	1.264
IFNg_GMCSF1	-0.27	1.458
Rv1432_day32	-0.017	0.332
Rv1565c_day32	0.477	0.482
secA2_input	-0.225	-0.178
delta_Rv3594	-1.014	-0.202
delta_Rv3717	-1.274	-0.321
delta_Rv3811	-1.06	-0.586
delta_Rv0954	-0.337	-0.295
PonA1	-1.005	0.614
EccD1_KO	0.855	0.812
EspI_KO	0.568	0.633
PE35_KO	0.373	0.534
PPE68_KO	0.589	0.195
glycerol2	-0.035	-0.581
lignocerate	0.086	-1.078
oleate	0.542	0.302
phosphatidylcholine	0.266	-0.294
acetate	-0.241	-1.282
glucAc	-0.187	-1.315
Rv0950ko	0.163	0.443
Rv1096ko	0.299	0.169
Rv3684ko	-0.635	0.144
delta_otsA_trehalose	-0.57	1.314