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 Rv1445c/devB:

update plot	correlation	link to info on gene
Rv0998/-	(cc=0.5231)	info on Rv0998/-
Rv2470/glbO	(cc=0.4825)	info on Rv2470/glbO
Rv3680/-	(cc=0.4788)	info on Rv3680/-
Rv1473/-	(cc=0.4776)	info on Rv1473/-
Rv2344c/dgt	(cc=0.472)	info on Rv2344c/dgt
Rv1963c/mce3R	(cc=0.4685)	info on Rv1963c/mce3R
Rv0038/-	(cc=0.4631)	info on Rv0038/-
Rv3754/tyrA	(cc=0.462)	info on Rv3754/tyrA
Rv1114/vapC32	(cc=0.4428)	info on Rv1114/vapC32
Rv1432/-	(cc=0.4421)	info on Rv1432/-

Correlation of Rv1445c/devB with Rv3680/-

Normalized LFCs for Rv1445c/devB:
(description and provenance of datasets)

	Rv1445c/devB	Rv3680/-
Fe_supp_jason_reseq	3.487	1.689
low_pH_jason_reseq	0.539	1.673
NO_jason_reseq	-1.089	0.0
B6_jason_reseq	-0.461	0.0
MHCII_jason_reseq	-0.663	0.0
Isoniazid02	0.422	-1.072
Rifampicin4	0.412	-0.474
Ethambutol3	-0.1	-0.59
Meropenem3	6.0	-0.21
Vancomycin16	-0.218	-0.464
Rv2680_day32	0.0	0.0
H37Rv_KO_MarP	-0.556	-0.766
hypoxia_3wks	-0.706	-0.55
hypoxia_6wks	0.33	-0.288
glycerol	1.403	2.455
cholesterol	0.435	1.612
AJ	0.797	0.0
Bibs02	1.751	1.015
Bibs02c	-0.399	1.822
BL6	-0.768	0.0
BL6a	0.0	1.812
BXD01	-0.552	0.358
BXD010	-0.787	0.128
BXD011	1.581	1.109
BXD03	0.076	0.75
BXD04	-0.42	0.34
BXD05	2.855	0.369
BXD06	-0.254	1.035
BXD07	0.475	0.38
BXD08	-0.079	0.253
BXD09	0.75	0.69
CAST	-1.185	0.0
CCcont	2.119	1.765
DS01	0.133	0.83
DS02	-1.119	0.217
DS04	-1.192	1.301
DS0c	2.875	0.413
GP01	0.492	0.0
GP02	-0.283	0.0
GP0c	-0.669	0.0
NOD	0.0	0.0
NZO	0.113	0.0
PWK	0.0	0.0
H37Rv_KO_CtpC	-0.835	0.162
H37Rv_KO_CtpD	-0.241	0.445
H37Rv_KO_Rv1272	-0.598	0.0
H37Rv_KO_SugABC	-0.26	0.768
H37Rv_KO_MbtN	-0.35	0.691
Trans05	-0.161	0.0
macrophage_unactivated	-2.273	0.436
IL1	-1.231	0.0
Rapamycin	-0.328	0.0
Tcell	-0.925	0.857
GMCSF	-1.096	0.0
IFNab	1.215	0.0
IFNg	-0.593	0.0
IFNg_GMCSF1	-1.756	0.0
Rv1432_day32	0.727	0.0
Rv1565c_day32	0.0	0.0
secA2_input	-0.775	-2.069
delta_Rv3594	3.284	1.895
delta_Rv3717	2.731	3.237
delta_Rv3811	3.123	2.787
delta_Rv0954	2.176	0.375
PonA1	1.981	1.599
EccD1_KO	2.263	0.635
EspI_KO	0.328	0.878
PE35_KO	1.383	0.735
PPE68_KO	2.937	1.245
glycerol2	-1.607	-0.193
lignocerate	-1.667	-0.168
oleate	-2.12	-0.196
phosphatidylcholine	-2.286	-0.193
acetate	1.24	0.743
glucAc	1.081	0.462
Rv0950ko	-0.528	-1.9
Rv1096ko	-0.817	-2.111
Rv3684ko	-1.985	-2.663
delta_otsA_trehalose	0.61	0.895