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 Rv2662/-:

update plot	correlation	link to info on gene
Rv2911/dacB2	(cc=0.4301)	info on Rv2911/dacB2
Rv0516c/-	(cc=0.3774)	info on Rv0516c/-
Rv2148c/-	(cc=0.356)	info on Rv2148c/-
Rv1477/ripA	(cc=0.3539)	info on Rv1477/ripA
Rv3856c/-	(cc=0.3485)	info on Rv3856c/-
Rv1527c/pks5	(cc=0.3478)	info on Rv1527c/pks5
Rv1089/PE10	(cc=0.3455)	info on Rv1089/PE10
Rv0969/ctpV	(cc=0.3432)	info on Rv0969/ctpV
Rv0630c/recB	(cc=0.3416)	info on Rv0630c/recB
Rv1961/-	(cc=0.3411)	info on Rv1961/-

Correlation of Rv2662/- with Rv1961/-

Normalized LFCs for Rv2662/-:
(description and provenance of datasets)

	Rv2662/-	Rv1961/-
Fe_supp_jason_reseq	1.86	-2.406
low_pH_jason_reseq	-0.547	-2.08
NO_jason_reseq	-0.05	0.184
B6_jason_reseq	-0.057	-1.989
MHCII_jason_reseq	-1.027	-1.677
Isoniazid02	0.009	0.236
Rifampicin4	-0.068	-0.06
Ethambutol3	-0.185	-0.407
Meropenem3	-0.165	-0.386
Vancomycin16	0.684	-0.114
Rv2680_day32	-0.228	-1.231
H37Rv_KO_MarP	0.862	-0.188
hypoxia_3wks	-0.124	-0.929
hypoxia_6wks	0.077	-0.411
glycerol	-0.161	0.13
cholesterol	-0.61	-0.233
AJ	0.844	0.533
Bibs02	0.984	0.242
Bibs02c	0.556	-0.399
BL6	0.161	0.758
BL6a	0.818	-0.118
BXD01	-0.368	-0.901
BXD010	0.495	-0.906
BXD011	-0.021	-0.524
BXD03	0.093	-0.369
BXD04	-0.511	-0.494
BXD05	1.146	0.076
BXD06	0.218	-0.241
BXD07	-0.015	0.272
BXD08	0.065	0.156
BXD09	0.293	-0.147
CAST	-1.086	0.287
CCcont	0.127	-0.33
DS01	0.84	0.527
DS02	1.084	0.158
DS04	2.195	0.843
DS0c	0.343	-0.789
GP01	3.083	0.532
GP02	0.266	1.445
GP0c	1.181	1.337
NOD	-1.261	-0.496
NZO	1.932	0.92
PWK	0.033	-1.091
H37Rv_KO_CtpC	0.683	0.04
H37Rv_KO_CtpD	-0.414	-0.241
H37Rv_KO_Rv1272	0.127	-0.254
H37Rv_KO_SugABC	0.865	0.123
H37Rv_KO_MbtN	1.546	-0.052
Trans05	-0.823	-0.223
macrophage_unactivated	1.272	-1.225
IL1	0.724	-0.219
Rapamycin	-0.853	0.031
Tcell	0.274	-0.277
GMCSF	-0.671	0.264
IFNab	0.889	0.184
IFNg	0.224	-0.377
IFNg_GMCSF1	1.04	0.063
Rv1432_day32	0.0	0.331
Rv1565c_day32	-1.657	-0.595
secA2_input	0.299	0.13
delta_Rv3594	0.642	0.171
delta_Rv3717	0.922	0.858
delta_Rv3811	0.916	1.316
delta_Rv0954	0.129	0.51
PonA1	-0.669	-0.609
EccD1_KO	0.52	-0.158
EspI_KO	0.111	-0.511
PE35_KO	1.698	-0.618
PPE68_KO	2.262	-0.154
glycerol2	0.193	-0.118
lignocerate	1.019	0.587
oleate	-2.066	-1.456
phosphatidylcholine	0.258	0.182
acetate	0.289	1.076
glucAc	0.333	1.194
Rv0950ko	0.844	0.917
Rv1096ko	1.858	0.66
Rv3684ko	1.611	0.357
delta_otsA_trehalose	0.957	-0.152