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 Rv3818/-

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

	Rv3150/nuoF	Rv3818/-
Fe_supp_jason_reseq	-1.514	-0.103
low_pH_jason_reseq	-0.313	-1.643
NO_jason_reseq	-0.252	-0.121
B6_jason_reseq	-1.087	-3.085
MHCII_jason_reseq	-1.509	-2.252
Isoniazid02	0.611	1.234
Rifampicin4	0.282	-3.579
Ethambutol3	-0.595	0.377
Meropenem3	-0.847	-0.771
Vancomycin16	-0.196	-3.321
Rv2680_day32	0.266	0.796
H37Rv_KO_MarP	-0.246	-2.515
hypoxia_3wks	1.097	2.592
hypoxia_6wks	0.754	2.946
glycerol	-0.471	-0.791
cholesterol	-0.216	0.645
AJ	-0.983	-1.837
Bibs02	0.55	0.474
Bibs02c	-0.23	0.067
BL6	1.845	1.975
BL6a	2.251	1.897
BXD01	1.864	1.939
BXD010	2.266	3.057
BXD011	2.05	2.413
BXD03	2.177	3.807
BXD04	2.337	2.431
BXD05	2.126	2.693
BXD06	2.045	2.991
BXD07	2.3	2.302
BXD08	2.274	1.691
BXD09	2.374	2.345
CAST	0.506	-0.794
CCcont	1.451	3.269
DS01	0.583	0.842
DS02	0.147	-0.072
DS04	0.426	2.485
DS0c	0.969	0.966
GP01	0.715	0.747
GP02	0.875	0.829
GP0c	1.092	1.295
NOD	-0.838	-0.88
NZO	0.38	-1.087
PWK	-0.142	-0.132
H37Rv_KO_CtpC	1.463	2.081
H37Rv_KO_CtpD	2.661	1.548
H37Rv_KO_Rv1272	1.929	1.572
H37Rv_KO_SugABC	1.426	1.297
H37Rv_KO_MbtN	1.537	4.543
Trans05	1.798	2.32
macrophage_unactivated	0.284	0.739
IL1	0.267	-0.341
Rapamycin	0.365	0.095
Tcell	0.746	0.443
GMCSF	0.388	0.51
IFNab	1.69	1.59
IFNg	-0.302	1.114
IFNg_GMCSF1	0.145	-0.641
Rv1432_day32	0.568	2.214
Rv1565c_day32	-0.208	0.218
secA2_input	-0.116	-1.506
delta_Rv3594	0.392	0.017
delta_Rv3717	0.299	1.251
delta_Rv3811	0.094	0.858
delta_Rv0954	-0.057	-2.768
PonA1	-0.39	-0.682
EccD1_KO	-0.474	-0.826
EspI_KO	-0.177	-0.245
PE35_KO	-0.467	0.324
PPE68_KO	0.0	-0.275
glycerol2	1.866	-0.738
lignocerate	-0.192	-1.76
oleate	2.076	-0.364
phosphatidylcholine	-0.221	-2.681
acetate	-0.263	0.188
glucAc	0.587	0.06
Rv0950ko	0.311	-1.426
Rv1096ko	0.639	-0.434
Rv3684ko	0.098	-0.472
delta_otsA_trehalose	0.965	-1.157