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 Rv0969/ctpV

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

	Rv2662/-	Rv0969/ctpV
Fe_supp_jason_reseq	1.86	-0.535
low_pH_jason_reseq	-0.547	-1.522
NO_jason_reseq	-0.05	-0.362
B6_jason_reseq	-0.057	-0.715
MHCII_jason_reseq	-1.027	-0.391
Isoniazid02	0.009	0.397
Rifampicin4	-0.068	-0.233
Ethambutol3	-0.185	0.581
Meropenem3	-0.165	0.492
Vancomycin16	0.684	-0.324
Rv2680_day32	-0.228	-0.154
H37Rv_KO_MarP	0.862	0.26
hypoxia_3wks	-0.124	-0.211
hypoxia_6wks	0.077	0.127
glycerol	-0.161	0.291
cholesterol	-0.61	0.358
AJ	0.844	0.44
Bibs02	0.984	0.648
Bibs02c	0.556	0.576
BL6	0.161	-0.084
BL6a	0.818	0.264
BXD01	-0.368	-0.556
BXD010	0.495	-0.288
BXD011	-0.021	-0.24
BXD03	0.093	-0.743
BXD04	-0.511	-0.305
BXD05	1.146	0.268
BXD06	0.218	-0.558
BXD07	-0.015	-0.301
BXD08	0.065	-0.299
BXD09	0.293	-0.216
CAST	-1.086	-0.534
CCcont	0.127	-0.391
DS01	0.84	0.303
DS02	1.084	0.15
DS04	2.195	0.611
DS0c	0.343	-0.039
GP01	3.083	0.358
GP02	0.266	-0.205
GP0c	1.181	-0.063
NOD	-1.261	-0.109
NZO	1.932	0.046
PWK	0.033	-0.483
H37Rv_KO_CtpC	0.683	0.139
H37Rv_KO_CtpD	-0.414	-0.802
H37Rv_KO_Rv1272	0.127	0.057
H37Rv_KO_SugABC	0.865	0.616
H37Rv_KO_MbtN	1.546	-0.877
Trans05	-0.823	-0.139
macrophage_unactivated	1.272	0.694
IL1	0.724	-0.11
Rapamycin	-0.853	0.11
Tcell	0.274	0.059
GMCSF	-0.671	-0.148
IFNab	0.889	0.163
IFNg	0.224	0.371
IFNg_GMCSF1	1.04	0.616
Rv1432_day32	0.0	0.322
Rv1565c_day32	-1.657	-0.264
secA2_input	0.299	0.892
delta_Rv3594	0.642	-0.32
delta_Rv3717	0.922	-0.328
delta_Rv3811	0.916	0.318
delta_Rv0954	0.129	0.143
PonA1	-0.669	0.324
EccD1_KO	0.52	0.382
EspI_KO	0.111	0.24
PE35_KO	1.698	0.292
PPE68_KO	2.262	0.218
glycerol2	0.193	0.15
lignocerate	1.019	0.144
oleate	-2.066	0.119
phosphatidylcholine	0.258	0.333
acetate	0.289	0.08
glucAc	0.333	0.157
Rv0950ko	0.844	0.223
Rv1096ko	1.858	1.077
Rv3684ko	1.611	0.609
delta_otsA_trehalose	0.957	2.032