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 Rv3150/nuoF:

update plot	correlation	link to info on gene
Rv3146/nuoB	(cc=0.8695)	info on Rv3146/nuoB
Rv3152/nuoH	(cc=0.8676)	info on Rv3152/nuoH
Rv3153/nuoI	(cc=0.8414)	info on Rv3153/nuoI
Rv3148/nuoD	(cc=0.8182)	info on Rv3148/nuoD
Rv3151/nuoG	(cc=0.7969)	info on Rv3151/nuoG
Rv3145/nuoA	(cc=0.7635)	info on Rv3145/nuoA
Rv3158/nuoN	(cc=0.7516)	info on Rv3158/nuoN
Rv3156/nuoL	(cc=0.7338)	info on Rv3156/nuoL
Rv3818/-	(cc=0.6963)	info on Rv3818/-
Rv1059/-	(cc=0.6944)	info on Rv1059/-

Correlation of Rv3150/nuoF with Rv3146/nuoB

Normalized LFCs for Rv3150/nuoF:
(description and provenance of datasets)

	Rv3150/nuoF	Rv3146/nuoB
Fe_supp_jason_reseq	-1.514	-1.318
low_pH_jason_reseq	-0.313	-0.895
NO_jason_reseq	-0.252	-0.63
B6_jason_reseq	-1.087	-2.02
MHCII_jason_reseq	-1.509	-2.204
Isoniazid02	0.611	-0.303
Rifampicin4	0.282	0.533
Ethambutol3	-0.595	1.094
Meropenem3	-0.847	-0.944
Vancomycin16	-0.196	0.0
Rv2680_day32	0.266	2.143
H37Rv_KO_MarP	-0.246	-0.08
hypoxia_3wks	1.097	1.228
hypoxia_6wks	0.754	0.528
glycerol	-0.471	0.669
cholesterol	-0.216	0.246
AJ	-0.983	-0.913
Bibs02	0.55	-2.215
Bibs02c	-0.23	-0.887
BL6	1.845	2.686
BL6a	2.251	3.008
BXD01	1.864	3.298
BXD010	2.266	3.288
BXD011	2.05	2.568
BXD03	2.177	2.99
BXD04	2.337	2.919
BXD05	2.126	3.2
BXD06	2.045	2.98
BXD07	2.3	3.309
BXD08	2.274	3.323
BXD09	2.374	3.314
CAST	0.506	0.829
CCcont	1.451	1.842
DS01	0.583	-0.202
DS02	0.147	-0.285
DS04	0.426	0.727
DS0c	0.969	0.443
GP01	0.715	1.199
GP02	0.875	0.444
GP0c	1.092	2.314
NOD	-0.838	0.381
NZO	0.38	0.118
PWK	-0.142	0.155
H37Rv_KO_CtpC	1.463	2.112
H37Rv_KO_CtpD	2.661	3.386
H37Rv_KO_Rv1272	1.929	2.5
H37Rv_KO_SugABC	1.426	2.905
H37Rv_KO_MbtN	1.537	3.496
Trans05	1.798	1.803
macrophage_unactivated	0.284	-0.196
IL1	0.267	-0.32
Rapamycin	0.365	-0.454
Tcell	0.746	-0.202
GMCSF	0.388	-0.536
IFNab	1.69	1.288
IFNg	-0.302	-0.016
IFNg_GMCSF1	0.145	-0.487
Rv1432_day32	0.568	-0.314
Rv1565c_day32	-0.208	-0.058
secA2_input	-0.116	-1.083
delta_Rv3594	0.392	0.268
delta_Rv3717	0.299	0.409
delta_Rv3811	0.094	-0.44
delta_Rv0954	-0.057	0.735
PonA1	-0.39	0.202
EccD1_KO	-0.474	-0.783
EspI_KO	-0.177	0.137
PE35_KO	-0.467	0.0
PPE68_KO	0.0	0.301
glycerol2	1.866	2.655
lignocerate	-0.192	-0.298
oleate	2.076	3.194
phosphatidylcholine	-0.221	-0.199
acetate	-0.263	0.037
glucAc	0.587	0.62
Rv0950ko	0.311	1.236
Rv1096ko	0.639	1.318
Rv3684ko	0.098	0.491
delta_otsA_trehalose	0.965	0.503