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 Rv2080/lppJ:

update plot	correlation	link to info on gene
Rv1861/-	(cc=0.5137)	info on Rv1861/-
Rv1517/-	(cc=0.4964)	info on Rv1517/-
Rv1966/mce3A	(cc=0.4903)	info on Rv1966/mce3A
Rv2735c/-	(cc=0.475)	info on Rv2735c/-
Rv3847/-	(cc=0.4633)	info on Rv3847/-
Rv1507c/-	(cc=0.4631)	info on Rv1507c/-
Rv1962A/vapB35	(cc=0.4595)	info on Rv1962A/vapB35
Rv3224/-	(cc=0.4466)	info on Rv3224/-
Rv2957/-	(cc=0.4413)	info on Rv2957/-
Rv1984c/cfp21	(cc=0.4348)	info on Rv1984c/cfp21

Correlation of Rv2080/lppJ with Rv1861/-

Normalized LFCs for Rv2080/lppJ:
(description and provenance of datasets)

	Rv2080/lppJ	Rv1861/-
Fe_supp_jason_reseq	-0.421	-0.117
low_pH_jason_reseq	-0.174	-1.655
NO_jason_reseq	0.281	0.428
B6_jason_reseq	-0.121	-1.122
MHCII_jason_reseq	0.159	-0.956
Isoniazid02	0.189	-0.723
Rifampicin4	0.138	-0.284
Ethambutol3	1.274	0.428
Meropenem3	-0.096	1.029
Vancomycin16	0.377	-0.342
Rv2680_day32	1.324	0.683
H37Rv_KO_MarP	-0.601	-0.428
hypoxia_3wks	0.303	0.63
hypoxia_6wks	-0.484	1.165
glycerol	-0.9	-2.422
cholesterol	-1.074	-0.936
AJ	0.247	0.155
Bibs02	0.397	0.057
Bibs02c	-0.975	-1.555
BL6	0.733	-0.072
BL6a	-0.096	-0.35
BXD01	0.355	0.581
BXD010	0.142	0.628
BXD011	0.453	0.659
BXD03	1.171	0.255
BXD04	0.312	0.521
BXD05	-0.505	-0.009
BXD06	0.428	0.903
BXD07	0.296	0.9
BXD08	0.497	0.989
BXD09	0.533	0.753
CAST	0.969	0.31
CCcont	-0.156	-0.188
DS01	0.455	0.445
DS02	0.019	-0.199
DS04	0.162	0.604
DS0c	-0.421	0.696
GP01	1.498	0.859
GP02	0.362	1.048
GP0c	0.547	0.809
NOD	0.543	0.861
NZO	-0.983	0.334
PWK	0.357	0.527
H37Rv_KO_CtpC	0.186	1.449
H37Rv_KO_CtpD	0.692	1.112
H37Rv_KO_Rv1272	1.607	0.338
H37Rv_KO_SugABC	1.653	1.671
H37Rv_KO_MbtN	0.224	0.74
Trans05	1.315	0.734
macrophage_unactivated	0.786	0.12
IL1	0.0	-0.617
Rapamycin	0.0	0.0
Tcell	-0.3	-0.192
GMCSF	-0.045	-0.396
IFNab	-0.26	-0.453
IFNg	-0.029	-0.363
IFNg_GMCSF1	0.465	-0.167
Rv1432_day32	0.077	0.386
Rv1565c_day32	-0.611	0.297
secA2_input	0.609	-0.194
delta_Rv3594	0.411	-0.11
delta_Rv3717	0.07	-0.41
delta_Rv3811	-0.388	-0.556
delta_Rv0954	-0.337	0.417
PonA1	0.801	-0.129
EccD1_KO	0.02	-0.046
EspI_KO	0.619	0.22
PE35_KO	-0.111	-0.064
PPE68_KO	-0.208	0.352
glycerol2	-0.116	-0.149
lignocerate	-0.437	-0.505
oleate	-0.173	0.411
phosphatidylcholine	0.099	-0.101
acetate	-0.843	-0.427
glucAc	-0.665	-1.002
Rv0950ko	-0.118	1.061
Rv1096ko	-0.256	-0.196
Rv3684ko	-0.337	-1.055
delta_otsA_trehalose	0.316	0.247