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 Rv2911/dacB2

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

	Rv2662/-	Rv2911/dacB2
Fe_supp_jason_reseq	1.86	0.406
low_pH_jason_reseq	-0.547	-1.26
NO_jason_reseq	-0.05	0.092
B6_jason_reseq	-0.057	-0.193
MHCII_jason_reseq	-1.027	-0.264
Isoniazid02	0.009	0.345
Rifampicin4	-0.068	0.041
Ethambutol3	-0.185	0.045
Meropenem3	-0.165	-0.319
Vancomycin16	0.684	1.849
Rv2680_day32	-0.228	0.404
H37Rv_KO_MarP	0.862	0.08
hypoxia_3wks	-0.124	0.821
hypoxia_6wks	0.077	1.054
glycerol	-0.161	0.774
cholesterol	-0.61	0.0
AJ	0.844	-0.318
Bibs02	0.984	0.599
Bibs02c	0.556	0.831
BL6	0.161	0.53
BL6a	0.818	0.773
BXD01	-0.368	-0.039
BXD010	0.495	0.989
BXD011	-0.021	0.667
BXD03	0.093	-0.026
BXD04	-0.511	0.036
BXD05	1.146	1.039
BXD06	0.218	0.274
BXD07	-0.015	0.675
BXD08	0.065	0.681
BXD09	0.293	0.132
CAST	-1.086	-0.504
CCcont	0.127	0.672
DS01	0.84	0.922
DS02	1.084	0.712
DS04	2.195	0.506
DS0c	0.343	-0.156
GP01	3.083	0.988
GP02	0.266	-0.278
GP0c	1.181	-0.163
NOD	-1.261	-0.332
NZO	1.932	-0.436
PWK	0.033	-0.551
H37Rv_KO_CtpC	0.683	0.772
H37Rv_KO_CtpD	-0.414	0.562
H37Rv_KO_Rv1272	0.127	-0.699
H37Rv_KO_SugABC	0.865	1.362
H37Rv_KO_MbtN	1.546	0.178
Trans05	-0.823	0.05
macrophage_unactivated	1.272	-0.11
IL1	0.724	0.777
Rapamycin	-0.853	0.552
Tcell	0.274	-0.352
GMCSF	-0.671	0.201
IFNab	0.889	0.426
IFNg	0.224	0.313
IFNg_GMCSF1	1.04	1.276
Rv1432_day32	0.0	0.413
Rv1565c_day32	-1.657	0.253
secA2_input	0.299	0.825
delta_Rv3594	0.642	0.405
delta_Rv3717	0.922	0.503
delta_Rv3811	0.916	0.302
delta_Rv0954	0.129	0.302
PonA1	-0.669	-0.306
EccD1_KO	0.52	0.895
EspI_KO	0.111	0.645
PE35_KO	1.698	1.26
PPE68_KO	2.262	1.251
glycerol2	0.193	0.283
lignocerate	1.019	0.339
oleate	-2.066	0.071
phosphatidylcholine	0.258	0.204
acetate	0.289	0.145
glucAc	0.333	0.471
Rv0950ko	0.844	0.775
Rv1096ko	1.858	0.995
Rv3684ko	1.611	1.081
delta_otsA_trehalose	0.957	0.942