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 Rv3652/PE_PGRS60:

update plot	correlation	link to info on gene
Rv0569/-	(cc=0.5626)	info on Rv0569/-
Rv1736c/narX	(cc=0.5455)	info on Rv1736c/narX
Rv0959/-	(cc=0.5353)	info on Rv0959/-
Rv1940/ribA1	(cc=0.5251)	info on Rv1940/ribA1
Rv2418c/-	(cc=0.5241)	info on Rv2418c/-
Rv2002/fabG3	(cc=0.5229)	info on Rv2002/fabG3
Rv0580c/-	(cc=0.5132)	info on Rv0580c/-
Rv2860c/glnA4	(cc=0.4998)	info on Rv2860c/glnA4
Rv2466c/-	(cc=0.4972)	info on Rv2466c/-
Rv1291c/-	(cc=0.4968)	info on Rv1291c/-

Correlation of Rv3652/PE_PGRS60 with Rv2002/fabG3

Normalized LFCs for Rv3652/PE_PGRS60:
(description and provenance of datasets)

	Rv3652/PE_PGRS60	Rv2002/fabG3
Fe_supp_jason_reseq	-0.27	-0.428
low_pH_jason_reseq	1.079	0.154
NO_jason_reseq	0.186	1.076
B6_jason_reseq	0.641	0.253
MHCII_jason_reseq	0.67	-0.136
Isoniazid02	0.33	1.014
Rifampicin4	-0.217	-0.482
Ethambutol3	0.169	1.17
Meropenem3	0.153	0.254
Vancomycin16	1.101	0.08
Rv2680_day32	2.801	2.861
H37Rv_KO_MarP	0.104	0.154
hypoxia_3wks	0.618	0.459
hypoxia_6wks	0.084	-0.109
glycerol	0.62	0.566
cholesterol	0.779	0.563
AJ	-0.111	0.079
Bibs02	0.699	1.183
Bibs02c	-0.573	0.227
BL6	-1.002	-0.121
BL6a	-0.512	0.067
BXD01	-0.249	-0.376
BXD010	-0.837	-0.724
BXD011	-0.305	-0.577
BXD03	-1.399	-0.875
BXD04	-0.409	0.014
BXD05	-0.534	-0.33
BXD06	-0.522	-0.835
BXD07	-0.716	-0.838
BXD08	-0.091	-0.86
BXD09	-0.683	-0.189
CAST	0.155	0.521
CCcont	-1.008	-1.206
DS01	0.712	1.251
DS02	-0.26	0.121
DS04	0.557	1.439
DS0c	-0.508	1.178
GP01	-0.386	0.107
GP02	0.445	0.24
GP0c	-0.907	-0.158
NOD	-0.462	0.801
NZO	0.262	-1.011
PWK	-0.618	-0.658
H37Rv_KO_CtpC	-2.385	-0.95
H37Rv_KO_CtpD	-1.86	0.0
H37Rv_KO_Rv1272	-0.668	0.514
H37Rv_KO_SugABC	-1.701	-1.05
H37Rv_KO_MbtN	-0.861	-0.623
Trans05	-1.511	0.549
macrophage_unactivated	0.114	0.71
IL1	1.21	0.943
Rapamycin	-0.377	-0.175
Tcell	-0.222	0.0
GMCSF	0.61	0.995
IFNab	1.233	0.221
IFNg	-0.139	-0.206
IFNg_GMCSF1	0.138	-0.562
Rv1432_day32	0.343	-0.648
Rv1565c_day32	0.722	-0.629
secA2_input	-0.258	0.423
delta_Rv3594	-0.376	0.814
delta_Rv3717	0.789	0.921
delta_Rv3811	-0.291	1.599
delta_Rv0954	0.247	0.362
PonA1	-0.455	-0.519
EccD1_KO	0.638	0.839
EspI_KO	0.428	0.211
PE35_KO	1.152	1.041
PPE68_KO	0.729	0.883
glycerol2	0.42	0.196
lignocerate	-0.161	-0.402
oleate	0.961	0.75
phosphatidylcholine	0.193	0.298
acetate	-0.091	-0.618
glucAc	-0.6	-1.292
Rv0950ko	-0.226	-0.7
Rv1096ko	0.422	0.392
Rv3684ko	0.177	0.819
delta_otsA_trehalose	1.871	-0.778