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 Rv2775/-:

update plot	correlation	link to info on gene
Rv1498c/-	(cc=0.6072)	info on Rv1498c/-
Rv2452c/-	(cc=0.5921)	info on Rv2452c/-
Rv2957/-	(cc=0.5567)	info on Rv2957/-
Rv1500/-	(cc=0.549)	info on Rv1500/-
Rv1583c/-	(cc=0.5471)	info on Rv1583c/-
Rv2267c/-	(cc=0.5409)	info on Rv2267c/-
Rv2881c/cdsA	(cc=0.5309)	info on Rv2881c/cdsA
Rv3628/ppa	(cc=0.5264)	info on Rv3628/ppa
Rv3429/PPE59	(cc=0.524)	info on Rv3429/PPE59
Rv1116/-	(cc=0.5156)	info on Rv1116/-

Correlation of Rv2775/- with Rv2881c/cdsA

Normalized LFCs for Rv2775/-:
(description and provenance of datasets)

	Rv2775/-	Rv2881c/cdsA
Fe_supp_jason_reseq	0.466	0.0
low_pH_jason_reseq	-0.037	0.284
NO_jason_reseq	-0.977	-1.42
B6_jason_reseq	0.469	-0.103
MHCII_jason_reseq	-0.364	-0.663
Isoniazid02	-0.389	0.0
Rifampicin4	-0.038	0.0
Ethambutol3	-0.276	0.0
Meropenem3	-1.548	0.0
Vancomycin16	-0.127	0.366
Rv2680_day32	-0.205	-0.131
H37Rv_KO_MarP	-0.666	-0.291
hypoxia_3wks	-0.817	0.0
hypoxia_6wks	0.058	0.0
glycerol	-1.814	-0.202
cholesterol	-1.544	-0.145
AJ	0.474	-0.232
Bibs02	-1.113	-0.183
Bibs02c	-0.1	-0.209
BL6	0.246	-0.125
BL6a	0.595	0.901
BXD01	0.083	0.328
BXD010	1.009	1.098
BXD011	0.952	2.555
BXD03	0.569	0.0
BXD04	0.432	-0.124
BXD05	2.161	1.667
BXD06	1.25	0.687
BXD07	0.675	0.126
BXD08	0.499	0.431
BXD09	0.951	0.802
CAST	0.592	0.581
CCcont	0.59	0.261
DS01	0.994	0.216
DS02	-0.378	0.704
DS04	0.037	-0.194
DS0c	-0.192	0.0
GP01	1.913	0.564
GP02	0.55	0.901
GP0c	1.296	1.788
NOD	1.394	1.731
NZO	0.162	-0.199
PWK	1.047	-0.196
H37Rv_KO_CtpC	0.599	0.637
H37Rv_KO_CtpD	1.142	1.951
H37Rv_KO_Rv1272	1.787	1.022
H37Rv_KO_SugABC	1.287	-0.099
H37Rv_KO_MbtN	0.538	-0.103
Trans05	1.467	2.824
macrophage_unactivated	0.524	-0.398
IL1	-0.35	-0.78
Rapamycin	0.964	-0.387
Tcell	-0.775	0.375
GMCSF	0.525	-0.333
IFNab	0.747	-0.795
IFNg	0.083	-0.703
IFNg_GMCSF1	0.019	-0.826
Rv1432_day32	0.113	0.0
Rv1565c_day32	0.199	0.0
secA2_input	0.172	-0.348
delta_Rv3594	-0.812	-0.997
delta_Rv3717	-1.117	0.081
delta_Rv3811	-1.056	-1.3
delta_Rv0954	-1.181	-0.274
PonA1	-2.209	-0.077
EccD1_KO	0.506	1.924
EspI_KO	1.269	0.633
PE35_KO	1.502	3.564
PPE68_KO	1.574	2.121
glycerol2	0.0	0.104
lignocerate	0.935	-0.96
oleate	-1.208	-0.483
phosphatidylcholine	0.629	-0.478
acetate	0.469	-1.31
glucAc	0.563	-0.456
Rv0950ko	0.389	0.211
Rv1096ko	0.178	-0.706
Rv3684ko	-0.098	-0.766
delta_otsA_trehalose	-0.085	-0.232