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 Rv3923c/rnpA:

update plot	correlation	link to info on gene
Rv3193c/-	(cc=0.7337)	info on Rv3193c/-
Rv2169c/-	(cc=0.7144)	info on Rv2169c/-
Rv2535c/pepQ	(cc=0.6465)	info on Rv2535c/pepQ
Rv3455c/truA	(cc=0.6443)	info on Rv3455c/truA
Rv2470/glbO	(cc=0.5759)	info on Rv2470/glbO
Rv0003/recF	(cc=0.5683)	info on Rv0003/recF
Rv1010/ksgA	(cc=0.5675)	info on Rv1010/ksgA
Rv2737c/recA	(cc=0.5399)	info on Rv2737c/recA
Rv0067c/-	(cc=0.5295)	info on Rv0067c/-
Rv1432/-	(cc=0.5187)	info on Rv1432/-

Correlation of Rv3923c/rnpA with Rv3193c/-

Normalized LFCs for Rv3923c/rnpA:
(description and provenance of datasets)

	Rv3923c/rnpA	Rv3193c/-
Fe_supp_jason_reseq	1.579	1.209
low_pH_jason_reseq	0.634	0.0
NO_jason_reseq	0.0	0.0
B6_jason_reseq	0.0	0.0
MHCII_jason_reseq	0.0	0.0
Isoniazid02	-0.146	-0.851
Rifampicin4	-1.21	-1.21
Ethambutol3	-0.251	-0.392
Meropenem3	0.315	-0.701
Vancomycin16	-1.186	-1.552
Rv2680_day32	0.0	0.0
H37Rv_KO_MarP	-0.116	-0.735
hypoxia_3wks	0.459	0.0
hypoxia_6wks	-0.549	0.0
glycerol	-0.654	0.202
cholesterol	-0.105	0.0
AJ	0.0	0.0
Bibs02	-0.592	0.0
Bibs02c	-0.677	0.0
BL6	-0.53	0.0
BL6a	-0.462	0.0
BXD01	-0.304	0.0
BXD010	-0.543	0.0
BXD011	-0.54	0.0
BXD03	-0.573	0.0
BXD04	-0.4	0.0
BXD05	-0.436	0.0
BXD06	-0.566	0.0
BXD07	-0.448	0.0
BXD08	-0.31	0.0
BXD09	-0.596	0.0
CAST	-0.537	0.0
CCcont	0.733	1.082
DS01	1.16	0.0
DS02	-0.922	0.0
DS04	-0.453	0.0
DS0c	-0.157	0.0
GP01	-0.418	0.0
GP02	-0.353	0.0
GP0c	-0.551	0.0
NOD	0.675	0.0
NZO	-0.646	0.0
PWK	-0.635	0.0
H37Rv_KO_CtpC	-0.688	0.0
H37Rv_KO_CtpD	-0.537	0.127
H37Rv_KO_Rv1272	-0.457	0.0
H37Rv_KO_SugABC	-0.42	0.0
H37Rv_KO_MbtN	0.31	0.103
Trans05	-0.095	0.0
macrophage_unactivated	0.0	0.0
IL1	-0.409	0.0
Rapamycin	-0.424	0.0
Tcell	-0.45	0.0
GMCSF	-0.364	0.0
IFNab	0.0	0.0
IFNg	-0.369	0.0
IFNg_GMCSF1	0.0	0.0
Rv1432_day32	0.0	0.0
Rv1565c_day32	0.0	0.0
secA2_input	-1.327	-0.992
delta_Rv3594	0.402	-0.34
delta_Rv3717	-0.736	-0.61
delta_Rv3811	-0.306	-0.721
delta_Rv0954	-1.172	-0.627
PonA1	-1.67	0.753
EccD1_KO	1.559	-0.697
EspI_KO	0.433	0.183
PE35_KO	0.648	2.298
PPE68_KO	2.038	1.731
glycerol2	-2.322	-4.572
lignocerate	-2.479	-3.653
oleate	-2.691	-4.626
phosphatidylcholine	-2.851	-4.041
acetate	0.17	-0.05
glucAc	0.41	0.44
Rv0950ko	-1.764	-0.929
Rv1096ko	-1.016	-0.929
Rv3684ko	0.0	-0.187
delta_otsA_trehalose	-0.329	-0.133