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 Rv2401/-:

update plot	correlation	link to info on gene
Rv2169c/-	(cc=0.528)	info on Rv2169c/-
Rv3193c/-	(cc=0.5168)	info on Rv3193c/-
Rv2346c/esxO	(cc=0.5109)	info on Rv2346c/esxO
Rv1578c/-	(cc=0.4973)	info on Rv1578c/-
Rv3696c/glpK	(cc=0.4951)	info on Rv3696c/glpK
Rv2709/-	(cc=0.4758)	info on Rv2709/-
Rv0011c/-	(cc=0.4738)	info on Rv0011c/-
Rv0598c/vapC27	(cc=0.4705)	info on Rv0598c/vapC27
Rv2793c/truB	(cc=0.4598)	info on Rv2793c/truB
Rv2228c/-	(cc=0.4534)	info on Rv2228c/-

Correlation of Rv2401/- with Rv3193c/-

Normalized LFCs for Rv2401/-:
(description and provenance of datasets)

	Rv2401/-	Rv3193c/-
Fe_supp_jason_reseq	1.001	1.209
low_pH_jason_reseq	1.261	0.0
NO_jason_reseq	2.079	0.0
B6_jason_reseq	2.108	0.0
MHCII_jason_reseq	-2.11	0.0
Isoniazid02	-0.258	-0.851
Rifampicin4	-0.742	-1.21
Ethambutol3	-0.597	-0.392
Meropenem3	-0.588	-0.701
Vancomycin16	-0.554	-1.552
Rv2680_day32	0.995	0.0
H37Rv_KO_MarP	0.267	-0.735
hypoxia_3wks	-0.486	0.0
hypoxia_6wks	2.397	0.0
glycerol	0.341	0.202
cholesterol	0.454	0.0
AJ	0.392	0.0
Bibs02	0.677	0.0
Bibs02c	-0.355	0.0
BL6	-0.723	0.0
BL6a	0.29	0.0
BXD01	-0.347	0.0
BXD010	0.543	0.0
BXD011	0.583	0.0
BXD03	-0.229	0.0
BXD04	0.627	0.0
BXD05	-0.405	0.0
BXD06	0.068	0.0
BXD07	1.803	0.0
BXD08	-0.225	0.0
BXD09	1.39	0.0
CAST	1.952	0.0
CCcont	0.149	1.082
DS01	2.452	0.0
DS02	3.341	0.0
DS04	0.645	0.0
DS0c	2.528	0.0
GP01	-1.012	0.0
GP02	0.0	0.0
GP0c	0.357	0.0
NOD	0.059	0.0
NZO	0.423	0.0
PWK	1.368	0.0
H37Rv_KO_CtpC	0.082	0.0
H37Rv_KO_CtpD	1.059	0.127
H37Rv_KO_Rv1272	-0.95	0.0
H37Rv_KO_SugABC	0.385	0.0
H37Rv_KO_MbtN	-0.921	0.103
Trans05	-1.434	0.0
macrophage_unactivated	-1.228	0.0
IL1	0.077	0.0
Rapamycin	0.236	0.0
Tcell	0.857	0.0
GMCSF	-0.85	0.0
IFNab	-0.417	0.0
IFNg	0.644	0.0
IFNg_GMCSF1	-3.224	0.0
Rv1432_day32	1.352	0.0
Rv1565c_day32	0.736	0.0
secA2_input	0.099	-0.992
delta_Rv3594	-1.479	-0.34
delta_Rv3717	-2.246	-0.61
delta_Rv3811	-1.862	-0.721
delta_Rv0954	-2.076	-0.627
PonA1	-0.091	0.753
EccD1_KO	0.901	-0.697
EspI_KO	-0.097	0.183
PE35_KO	2.818	2.298
PPE68_KO	2.048	1.731
glycerol2	-2.474	-4.572
lignocerate	-1.689	-3.653
oleate	-2.504	-4.626
phosphatidylcholine	-2.473	-4.041
acetate	-0.465	-0.05
glucAc	-0.187	0.44
Rv0950ko	-1.517	-0.929
Rv1096ko	-1.034	-0.929
Rv3684ko	-3.331	-0.187
delta_otsA_trehalose	-0.864	-0.133