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 Rv1583c/-

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

	Rv2775/-	Rv1583c/-
Fe_supp_jason_reseq	0.466	0.515
low_pH_jason_reseq	-0.037	1.549
NO_jason_reseq	-0.977	0.832
B6_jason_reseq	0.469	-2.401
MHCII_jason_reseq	-0.364	-1.772
Isoniazid02	-0.389	0.789
Rifampicin4	-0.038	1.18
Ethambutol3	-0.276	0.676
Meropenem3	-1.548	-0.246
Vancomycin16	-0.127	0.324
Rv2680_day32	-0.205	-1.26
H37Rv_KO_MarP	-0.666	0.107
hypoxia_3wks	-0.817	-0.977
hypoxia_6wks	0.058	0.672
glycerol	-1.814	0.0
cholesterol	-1.544	-0.46
AJ	0.474	-1.071
Bibs02	-1.113	-0.991
Bibs02c	-0.1	0.743
BL6	0.246	3.191
BL6a	0.595	1.936
BXD01	0.083	1.298
BXD010	1.009	1.592
BXD011	0.952	2.091
BXD03	0.569	2.033
BXD04	0.432	1.324
BXD05	2.161	1.302
BXD06	1.25	1.925
BXD07	0.675	2.073
BXD08	0.499	1.806
BXD09	0.951	1.625
CAST	0.592	0.736
CCcont	0.59	2.504
DS01	0.994	0.962
DS02	-0.378	0.054
DS04	0.037	1.612
DS0c	-0.192	-1.798
GP01	1.913	1.857
GP02	0.55	1.808
GP0c	1.296	2.036
NOD	1.394	0.797
NZO	0.162	0.673
PWK	1.047	-0.905
H37Rv_KO_CtpC	0.599	1.404
H37Rv_KO_CtpD	1.142	3.186
H37Rv_KO_Rv1272	1.787	0.795
H37Rv_KO_SugABC	1.287	1.851
H37Rv_KO_MbtN	0.538	0.987
Trans05	1.467	1.01
macrophage_unactivated	0.524	0.559
IL1	-0.35	0.0
Rapamycin	0.964	0.862
Tcell	-0.775	0.469
GMCSF	0.525	0.805
IFNab	0.747	-0.115
IFNg	0.083	1.219
IFNg_GMCSF1	0.019	0.537
Rv1432_day32	0.113	1.454
Rv1565c_day32	0.199	0.526
secA2_input	0.172	-0.227
delta_Rv3594	-0.812	-1.637
delta_Rv3717	-1.117	-0.945
delta_Rv3811	-1.056	-0.448
delta_Rv0954	-1.181	-0.472
PonA1	-2.209	-0.396
EccD1_KO	0.506	2.088
EspI_KO	1.269	1.141
PE35_KO	1.502	1.523
PPE68_KO	1.574	1.638
glycerol2	0.0	1.813
lignocerate	0.935	2.527
oleate	-1.208	-2.562
phosphatidylcholine	0.629	1.909
acetate	0.469	2.818
glucAc	0.563	2.145
Rv0950ko	0.389	0.826
Rv1096ko	0.178	-1.197
Rv3684ko	-0.098	-1.251
delta_otsA_trehalose	-0.085	0.204