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 Rv3188/-

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

	Rv2800/-	Rv3188/-
Fe_supp_jason_reseq	-0.167	0.395
low_pH_jason_reseq	-0.545	0.611
NO_jason_reseq	-0.236	-0.139
B6_jason_reseq	0.485	0.151
MHCII_jason_reseq	0.614	1.439
Isoniazid02	0.164	-0.134
Rifampicin4	0.55	-0.677
Ethambutol3	-0.216	-0.016
Meropenem3	0.079	-0.031
Vancomycin16	0.3	-0.393
Rv2680_day32	0.092	-0.21
H37Rv_KO_MarP	0.236	0.12
hypoxia_3wks	0.363	0.223
hypoxia_6wks	-0.367	-0.184
glycerol	0.424	-0.518
cholesterol	0.064	0.268
AJ	0.136	0.38
Bibs02	-0.668	-0.837
Bibs02c	0.062	1.088
BL6	0.134	0.917
BL6a	-0.108	0.915
BXD01	-0.223	0.476
BXD010	-0.253	0.255
BXD011	-0.465	0.443
BXD03	0.464	0.683
BXD04	0.717	1.355
BXD05	-0.041	-0.33
BXD06	-0.182	0.862
BXD07	-0.097	0.246
BXD08	0.279	-0.415
BXD09	-0.179	0.023
CAST	0.017	-0.47
CCcont	-0.366	0.93
DS01	1.076	1.324
DS02	0.613	0.945
DS04	0.758	0.687
DS0c	0.946	0.52
GP01	0.606	-0.427
GP02	-0.157	-1.837
GP0c	-0.211	-0.033
NOD	2.379	2.211
NZO	-0.172	-2.208
PWK	-0.185	-0.924
H37Rv_KO_CtpC	-0.321	0.515
H37Rv_KO_CtpD	-0.462	1.259
H37Rv_KO_Rv1272	-0.169	-0.288
H37Rv_KO_SugABC	0.977	0.608
H37Rv_KO_MbtN	-0.754	0.87
Trans05	-0.212	0.59
macrophage_unactivated	2.108	2.058
IL1	-0.11	0.332
Rapamycin	-0.141	0.055
Tcell	-0.502	-0.27
GMCSF	-0.048	-0.615
IFNab	0.242	-0.426
IFNg	-0.636	-1.264
IFNg_GMCSF1	0.085	-0.352
Rv1432_day32	0.19	-0.961
Rv1565c_day32	-0.071	-0.264
secA2_input	-1.115	0.141
delta_Rv3594	-0.35	-0.271
delta_Rv3717	0.015	-0.035
delta_Rv3811	-0.193	-0.87
delta_Rv0954	0.11	-0.283
PonA1	0.337	-1.929
EccD1_KO	0.628	1.687
EspI_KO	0.302	0.074
PE35_KO	0.595	1.444
PPE68_KO	0.739	1.901
glycerol2	-0.436	0.06
lignocerate	-0.483	0.789
oleate	-0.098	0.024
phosphatidylcholine	-0.197	0.584
acetate	-0.057	0.141
glucAc	-0.52	1.043
Rv0950ko	-0.485	-0.727
Rv1096ko	0.323	0.555
Rv3684ko	-0.046	0.082
delta_otsA_trehalose	-0.343	-1.196