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 Rv0114/gmhB:

update plot	correlation	link to info on gene
Rv3429/PPE59	(cc=0.5625)	info on Rv3429/PPE59
Rv1593c/-	(cc=0.5324)	info on Rv1593c/-
Rv1500/-	(cc=0.5287)	info on Rv1500/-
Rv3210c/-	(cc=0.5193)	info on Rv3210c/-
Rv0305c/PPE6	(cc=0.5174)	info on Rv0305c/PPE6
Rv3528c/-	(cc=0.5168)	info on Rv3528c/-
Rv3524/-	(cc=0.5099)	info on Rv3524/-
Rv1981c/nrdF1	(cc=0.5018)	info on Rv1981c/nrdF1
Rv0028/-	(cc=0.4889)	info on Rv0028/-
Rv0059/-	(cc=0.4872)	info on Rv0059/-

Correlation of Rv0114/gmhB with Rv3524/-

Normalized LFCs for Rv0114/gmhB:
(description and provenance of datasets)

	Rv0114/gmhB	Rv3524/-
Fe_supp_jason_reseq	0.718	0.391
low_pH_jason_reseq	-0.632	-0.271
NO_jason_reseq	1.271	0.181
B6_jason_reseq	0.594	0.534
MHCII_jason_reseq	0.439	0.474
Isoniazid02	-0.051	-0.239
Rifampicin4	-0.046	-0.444
Ethambutol3	-0.129	-1.001
Meropenem3	1.923	-0.698
Vancomycin16	0.409	-0.345
Rv2680_day32	0.962	0.121
H37Rv_KO_MarP	0.069	-0.042
hypoxia_3wks	-0.73	0.02
hypoxia_6wks	-0.079	0.136
glycerol	-0.762	-0.645
cholesterol	-0.144	-0.696
AJ	0.849	-0.131
Bibs02	0.188	0.118
Bibs02c	1.173	0.668
BL6	1.019	0.761
BL6a	1.633	0.465
BXD01	0.578	0.542
BXD010	0.796	0.707
BXD011	2.605	0.492
BXD03	1.583	0.38
BXD04	1.206	0.599
BXD05	0.811	0.549
BXD06	1.011	0.527
BXD07	1.313	0.715
BXD08	0.994	0.706
BXD09	0.777	0.527
CAST	0.566	0.157
CCcont	0.79	0.577
DS01	0.503	0.127
DS02	0.487	0.158
DS04	1.088	0.461
DS0c	0.544	0.288
GP01	0.688	0.428
GP02	0.101	-0.359
GP0c	0.118	-0.251
NOD	1.526	0.036
NZO	0.457	-0.016
PWK	0.128	0.142
H37Rv_KO_CtpC	0.805	0.075
H37Rv_KO_CtpD	2.513	1.135
H37Rv_KO_Rv1272	1.842	1.129
H37Rv_KO_SugABC	2.029	0.097
H37Rv_KO_MbtN	0.753	-0.181
Trans05	1.298	0.248
macrophage_unactivated	0.508	0.041
IL1	-0.4	-0.092
Rapamycin	0.313	0.068
Tcell	0.772	-0.013
GMCSF	1.648	0.148
IFNab	0.671	0.067
IFNg	0.214	-0.035
IFNg_GMCSF1	0.198	-0.013
Rv1432_day32	0.435	-0.317
Rv1565c_day32	-2.3	0.0
secA2_input	-0.822	-0.814
delta_Rv3594	0.176	-0.493
delta_Rv3717	0.841	-0.301
delta_Rv3811	-0.052	-0.193
delta_Rv0954	0.863	0.058
PonA1	-0.166	-0.364
EccD1_KO	0.115	-1.121
EspI_KO	0.083	-0.525
PE35_KO	0.344	-1.012
PPE68_KO	0.429	-0.538
glycerol2	1.023	0.056
lignocerate	1.24	0.346
oleate	0.119	0.021
phosphatidylcholine	1.042	0.272
acetate	0.853	-0.166
glucAc	0.887	0.572
Rv0950ko	1.269	0.567
Rv1096ko	0.145	0.018
Rv3684ko	0.881	0.891
delta_otsA_trehalose	-0.281	0.604