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 Rv1990A/-:

update plot	correlation	link to info on gene
Rv2039c/-	(cc=0.5673)	info on Rv2039c/-
Rv2929/-	(cc=0.5487)	info on Rv2929/-
Rv0235c/-	(cc=0.5038)	info on Rv0235c/-
Rv1076/lipU	(cc=0.5025)	info on Rv1076/lipU
Rv0973c/accA2	(cc=0.4986)	info on Rv0973c/accA2
Rv2044c/-	(cc=0.4923)	info on Rv2044c/-
Rv2677c/hemY	(cc=0.4746)	info on Rv2677c/hemY
Rv3545c/cyp125	(cc=0.4737)	info on Rv3545c/cyp125
Rv2575/-	(cc=0.4711)	info on Rv2575/-
Rv1870c/-	(cc=0.4663)	info on Rv1870c/-

Correlation of Rv1990A/- with Rv1076/lipU

Normalized LFCs for Rv1990A/-:
(description and provenance of datasets)

	Rv1990A/-	Rv1076/lipU
Fe_supp_jason_reseq	0.0	-0.758
low_pH_jason_reseq	-0.664	-0.572
NO_jason_reseq	0.189	-0.116
B6_jason_reseq	-1.972	-2.089
MHCII_jason_reseq	-1.757	-1.507
Isoniazid02	3.843	0.432
Rifampicin4	0.344	-0.531
Ethambutol3	0.426	-0.204
Meropenem3	-0.214	0.207
Vancomycin16	0.109	-0.133
Rv2680_day32	-2.044	0.01
H37Rv_KO_MarP	0.234	0.0
hypoxia_3wks	0.156	0.459
hypoxia_6wks	-0.013	0.58
glycerol	-0.524	-0.679
cholesterol	-1.205	-0.138
AJ	-0.718	-0.467
Bibs02	-3.247	-0.487
Bibs02c	-1.288	0.158
BL6	0.304	1.495
BL6a	0.522	0.822
BXD01	1.7	0.918
BXD010	1.82	1.454
BXD011	0.735	0.801
BXD03	0.678	1.436
BXD04	0.62	0.88
BXD05	1.24	1.378
BXD06	0.582	1.131
BXD07	1.093	1.174
BXD08	0.602	1.727
BXD09	0.977	1.367
CAST	-0.415	-0.123
CCcont	0.528	0.939
DS01	0.202	-0.127
DS02	-0.729	-0.438
DS04	-1.876	-1.036
DS0c	0.198	-0.116
GP01	-0.48	1.274
GP02	1.816	0.499
GP0c	0.506	0.721
NOD	1.196	-0.599
NZO	-1.37	0.444
PWK	-0.728	-0.624
H37Rv_KO_CtpC	1.267	1.27
H37Rv_KO_CtpD	-0.307	1.152
H37Rv_KO_Rv1272	0.905	-0.155
H37Rv_KO_SugABC	1.82	-0.446
H37Rv_KO_MbtN	-0.511	0.162
Trans05	1.228	1.311
macrophage_unactivated	1.701	0.3
IL1	0.383	0.047
Rapamycin	0.491	0.172
Tcell	0.16	0.261
GMCSF	-0.417	0.525
IFNab	0.076	1.206
IFNg	0.053	0.946
IFNg_GMCSF1	-0.242	-0.157
Rv1432_day32	0.18	0.597
Rv1565c_day32	0.0	0.077
secA2_input	1.014	1.268
delta_Rv3594	0.333	-0.087
delta_Rv3717	0.313	0.274
delta_Rv3811	0.744	0.04
delta_Rv0954	-0.37	0.791
PonA1	-0.247	0.182
EccD1_KO	-0.312	0.569
EspI_KO	-0.111	0.61
PE35_KO	0.545	0.385
PPE68_KO	-0.797	0.048
glycerol2	0.722	0.839
lignocerate	0.781	0.841
oleate	0.98	1.355
phosphatidylcholine	0.79	1.133
acetate	0.617	0.116
glucAc	0.333	0.0
Rv0950ko	-0.054	-0.069
Rv1096ko	0.573	0.172
Rv3684ko	-0.16	-0.039
delta_otsA_trehalose	0.07	0.333