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 Rv1420/uvrC:

update plot	correlation	link to info on gene
Rv1421/-	(cc=0.7484)	info on Rv1421/-
Rv1908c/katG	(cc=0.6662)	info on Rv1908c/katG
Rv0019c/fhaB	(cc=0.6586)	info on Rv0019c/fhaB
Rv1633/uvrB	(cc=0.657)	info on Rv1633/uvrB
Rv3715c/recR	(cc=0.6191)	info on Rv3715c/recR
Rv3311/-	(cc=0.6153)	info on Rv3311/-
Rv3864/espE	(cc=0.5896)	info on Rv3864/espE
Rv2190c/-	(cc=0.5867)	info on Rv2190c/-
Rv1364c/-	(cc=0.5835)	info on Rv1364c/-
Rv0016c/pbpA	(cc=0.576)	info on Rv0016c/pbpA

Correlation of Rv1420/uvrC with Rv1908c/katG

Normalized LFCs for Rv1420/uvrC:
(description and provenance of datasets)

	Rv1420/uvrC	Rv1908c/katG
Fe_supp_jason_reseq	1.773	2.303
low_pH_jason_reseq	0.085	-0.44
NO_jason_reseq	-1.467	-0.69
B6_jason_reseq	-0.799	-0.292
MHCII_jason_reseq	-0.217	-0.257
Isoniazid02	-0.457	0.0
Rifampicin4	0.699	0.0
Ethambutol3	-1.07	0.0
Meropenem3	-0.522	0.0
Vancomycin16	0.162	0.0
Rv2680_day32	0.222	0.0
H37Rv_KO_MarP	-2.503	-1.722
hypoxia_3wks	0.949	-0.977
hypoxia_6wks	0.867	-2.714
glycerol	0.136	0.0
cholesterol	0.711	0.0
AJ	-0.541	0.0
Bibs02	1.827	0.0
Bibs02c	0.399	0.0
BL6	0.816	0.238
BL6a	1.291	0.544
BXD01	1.666	0.248
BXD010	-0.191	0.0
BXD011	1.128	0.854
BXD03	1.157	0.0
BXD04	-0.09	0.34
BXD05	0.539	0.661
BXD06	0.92	0.469
BXD07	0.555	0.0
BXD08	0.653	0.365
BXD09	0.916	0.69
CAST	-0.976	0.0
CCcont	2.214	3.165
DS01	-0.171	0.0
DS02	-0.922	0.0
DS04	0.777	0.953
DS0c	0.652	0.0
GP01	-0.147	0.0
GP02	0.292	0.0
GP0c	0.748	0.0
NOD	-0.524	0.0
NZO	0.0	0.0
PWK	-0.293	0.0
H37Rv_KO_CtpC	1.232	0.446
H37Rv_KO_CtpD	0.381	0.703
H37Rv_KO_Rv1272	1.409	0.141
H37Rv_KO_SugABC	1.015	0.42
H37Rv_KO_MbtN	1.942	2.414
Trans05	1.847	0.359
macrophage_unactivated	0.253	0.0
IL1	-0.658	0.0
Rapamycin	0.7	0.0
Tcell	1.769	0.0
GMCSF	-0.224	0.0
IFNab	2.276	0.417
IFNg	0.882	0.0
IFNg_GMCSF1	0.716	0.0
Rv1432_day32	-0.568	-0.494
Rv1565c_day32	0.873	0.0
secA2_input	0.276	0.67
delta_Rv3594	1.398	0.907
delta_Rv3717	1.754	0.784
delta_Rv3811	1.895	0.812
delta_Rv0954	0.282	0.842
PonA1	0.284	-0.419
EccD1_KO	-1.582	-4.969
EspI_KO	-1.124	-4.743
PE35_KO	0.184	1.374
PPE68_KO	-0.586	0.275
glycerol2	-1.574	-3.698
lignocerate	-1.959	-2.548
oleate	-2.181	-3.077
phosphatidylcholine	-2.06	-3.546
acetate	-0.248	0.253
glucAc	-0.238	-0.375
Rv0950ko	-1.288	-1.212
Rv1096ko	-0.057	-1.493
Rv3684ko	-0.445	-0.298
delta_otsA_trehalose	1.089	0.153