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 Rv1421/-:

update plot	correlation	link to info on gene
Rv1420/uvrC	(cc=0.7484)	info on Rv1420/uvrC
Rv0998/-	(cc=0.6731)	info on Rv0998/-
Rv2553c/-	(cc=0.6447)	info on Rv2553c/-
Rv3680/-	(cc=0.6354)	info on Rv3680/-
Rv0019c/fhaB	(cc=0.6324)	info on Rv0019c/fhaB
Rv0017c/rodA	(cc=0.5958)	info on Rv0017c/rodA
Rv1512/epiA	(cc=0.5948)	info on Rv1512/epiA
Rv0018c/pstP	(cc=0.5857)	info on Rv0018c/pstP
Rv2131c/cysQ	(cc=0.5843)	info on Rv2131c/cysQ
Rv0016c/pbpA	(cc=0.5841)	info on Rv0016c/pbpA

Correlation of Rv1421/- with Rv3680/-

Normalized LFCs for Rv1421/-:
(description and provenance of datasets)

	Rv1421/-	Rv3680/-
Fe_supp_jason_reseq	1.76	1.689
low_pH_jason_reseq	3.244	1.673
NO_jason_reseq	-1.864	0.0
B6_jason_reseq	-0.189	0.0
MHCII_jason_reseq	1.054	0.0
Isoniazid02	-0.247	-1.072
Rifampicin4	0.355	-0.474
Ethambutol3	-2.404	-0.59
Meropenem3	-1.17	-0.21
Vancomycin16	0.565	-0.464
Rv2680_day32	0.0	0.0
H37Rv_KO_MarP	-3.348	-0.766
hypoxia_3wks	1.934	-0.55
hypoxia_6wks	2.088	-0.288
glycerol	2.047	2.455
cholesterol	1.916	1.612
AJ	-0.232	0.0
Bibs02	3.974	1.015
Bibs02c	1.795	1.822
BL6	0.845	0.0
BL6a	1.934	1.812
BXD01	0.0	0.358
BXD010	0.0	0.128
BXD011	0.412	1.109
BXD03	-0.135	0.75
BXD04	0.312	0.34
BXD05	0.768	0.369
BXD06	0.523	1.035
BXD07	0.712	0.38
BXD08	0.121	0.253
BXD09	0.0	0.69
CAST	-0.23	0.0
CCcont	3.297	1.765
DS01	0.595	0.83
DS02	0.199	0.217
DS04	2.513	1.301
DS0c	0.85	0.413
GP01	1.767	0.0
GP02	0.076	0.0
GP0c	0.942	0.0
NOD	-0.225	0.0
NZO	-0.199	0.0
PWK	-0.196	0.0
H37Rv_KO_CtpC	0.739	0.162
H37Rv_KO_CtpD	1.454	0.445
H37Rv_KO_Rv1272	0.457	0.0
H37Rv_KO_SugABC	1.31	0.768
H37Rv_KO_MbtN	1.116	0.691
Trans05	0.228	0.0
macrophage_unactivated	-0.451	0.436
IL1	-1.898	0.0
Rapamycin	0.083	0.0
Tcell	0.424	0.857
GMCSF	0.718	0.0
IFNab	3.105	0.0
IFNg	-0.382	0.0
IFNg_GMCSF1	-0.085	0.0
Rv1432_day32	-0.18	0.0
Rv1565c_day32	0.218	0.0
secA2_input	-0.595	-2.069
delta_Rv3594	2.688	1.895
delta_Rv3717	4.737	3.237
delta_Rv3811	3.169	2.787
delta_Rv0954	1.193	0.375
PonA1	-0.119	1.599
EccD1_KO	-1.266	0.635
EspI_KO	-1.711	0.878
PE35_KO	-0.473	0.735
PPE68_KO	-1.296	1.245
glycerol2	-2.081	-0.193
lignocerate	-1.808	-0.168
oleate	-2.105	-0.196
phosphatidylcholine	-2.08	-0.193
acetate	-0.579	0.743
glucAc	-0.229	0.462
Rv0950ko	-4.921	-1.9
Rv1096ko	-0.935	-2.111
Rv3684ko	-1.765	-2.663
delta_otsA_trehalose	0.564	0.895