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 Rv2800/-:

update plot	correlation	link to info on gene
Rv2976c/ung	(cc=0.4519)	info on Rv2976c/ung
Rv0375c/-	(cc=0.4494)	info on Rv0375c/-
Rv2601/speE	(cc=0.4322)	info on Rv2601/speE
Rv3188/-	(cc=0.4268)	info on Rv3188/-
Rv0141c/-	(cc=0.4122)	info on Rv0141c/-
Rv3233c/-	(cc=0.3932)	info on Rv3233c/-
Rv2598/-	(cc=0.3917)	info on Rv2598/-
Rv0557/mgtA	(cc=0.3856)	info on Rv0557/mgtA
Rv3333c/-	(cc=0.3808)	info on Rv3333c/-
Rv1125/-	(cc=0.3772)	info on Rv1125/-

Correlation of Rv2800/- with Rv1125/-

Normalized LFCs for Rv2800/-:
(description and provenance of datasets)

	Rv2800/-	Rv1125/-
Fe_supp_jason_reseq	-0.167	-0.448
low_pH_jason_reseq	-0.545	0.167
NO_jason_reseq	-0.236	-0.428
B6_jason_reseq	0.485	0.929
MHCII_jason_reseq	0.614	1.89
Isoniazid02	0.164	-1.603
Rifampicin4	0.55	0.43
Ethambutol3	-0.216	-1.75
Meropenem3	0.079	-1.635
Vancomycin16	0.3	-0.735
Rv2680_day32	0.092	-0.091
H37Rv_KO_MarP	0.236	0.879
hypoxia_3wks	0.363	0.443
hypoxia_6wks	-0.367	0.34
glycerol	0.424	1.055
cholesterol	0.064	-0.345
AJ	0.136	0.334
Bibs02	-0.668	0.136
Bibs02c	0.062	0.659
BL6	0.134	0.832
BL6a	-0.108	0.075
BXD01	-0.223	0.274
BXD010	-0.253	-0.274
BXD011	-0.465	-0.272
BXD03	0.464	-0.424
BXD04	0.717	0.298
BXD05	-0.041	0.194
BXD06	-0.182	0.124
BXD07	-0.097	-0.296
BXD08	0.279	0.214
BXD09	-0.179	-0.204
CAST	0.017	-0.492
CCcont	-0.366	0.533
DS01	1.076	1.369
DS02	0.613	0.685
DS04	0.758	0.214
DS0c	0.946	1.328
GP01	0.606	-0.284
GP02	-0.157	-0.635
GP0c	-0.211	-0.342
NOD	2.379	1.092
NZO	-0.172	-0.678
PWK	-0.185	-0.038
H37Rv_KO_CtpC	-0.321	-0.387
H37Rv_KO_CtpD	-0.462	-1.696
H37Rv_KO_Rv1272	-0.169	0.444
H37Rv_KO_SugABC	0.977	-0.575
H37Rv_KO_MbtN	-0.754	-1.245
Trans05	-0.212	0.049
macrophage_unactivated	2.108	0.0
IL1	-0.11	0.721
Rapamycin	-0.141	0.681
Tcell	-0.502	-1.248
GMCSF	-0.048	1.281
IFNab	0.242	0.142
IFNg	-0.636	0.307
IFNg_GMCSF1	0.085	0.952
Rv1432_day32	0.19	0.271
Rv1565c_day32	-0.071	-0.398
secA2_input	-1.115	-1.288
delta_Rv3594	-0.35	0.698
delta_Rv3717	0.015	0.101
delta_Rv3811	-0.193	-0.403
delta_Rv0954	0.11	0.053
PonA1	0.337	0.0
EccD1_KO	0.628	1.411
EspI_KO	0.302	1.104
PE35_KO	0.595	1.129
PPE68_KO	0.739	0.813
glycerol2	-0.436	0.113
lignocerate	-0.483	0.704
oleate	-0.098	0.058
phosphatidylcholine	-0.197	0.625
acetate	-0.057	0.555
glucAc	-0.52	0.311
Rv0950ko	-0.485	0.793
Rv1096ko	0.323	0.995
Rv3684ko	-0.046	0.632
delta_otsA_trehalose	-0.343	-0.147