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 Rv1870c/-

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

	Rv1990A/-	Rv1870c/-
Fe_supp_jason_reseq	0.0	0.065
low_pH_jason_reseq	-0.664	0.423
NO_jason_reseq	0.189	-0.441
B6_jason_reseq	-1.972	-0.984
MHCII_jason_reseq	-1.757	-0.545
Isoniazid02	3.843	1.378
Rifampicin4	0.344	-0.273
Ethambutol3	0.426	1.971
Meropenem3	-0.214	0.072
Vancomycin16	0.109	-0.462
Rv2680_day32	-2.044	-0.858
H37Rv_KO_MarP	0.234	0.103
hypoxia_3wks	0.156	-0.159
hypoxia_6wks	-0.013	0.461
glycerol	-0.524	-0.547
cholesterol	-1.205	-0.614
AJ	-0.718	-0.424
Bibs02	-3.247	-1.472
Bibs02c	-1.288	0.537
BL6	0.304	0.418
BL6a	0.522	0.726
BXD01	1.7	0.563
BXD010	1.82	1.102
BXD011	0.735	0.675
BXD03	0.678	0.607
BXD04	0.62	0.748
BXD05	1.24	0.599
BXD06	0.582	0.744
BXD07	1.093	0.239
BXD08	0.602	0.646
BXD09	0.977	0.712
CAST	-0.415	0.28
CCcont	0.528	0.652
DS01	0.202	-0.077
DS02	-0.729	-0.364
DS04	-1.876	1.131
DS0c	0.198	0.277
GP01	-0.48	-0.039
GP02	1.816	-1.333
GP0c	0.506	-0.268
NOD	1.196	-0.376
NZO	-1.37	-0.38
PWK	-0.728	0.338
H37Rv_KO_CtpC	1.267	0.341
H37Rv_KO_CtpD	-0.307	0.19
H37Rv_KO_Rv1272	0.905	0.868
H37Rv_KO_SugABC	1.82	0.679
H37Rv_KO_MbtN	-0.511	0.723
Trans05	1.228	1.342
macrophage_unactivated	1.701	0.445
IL1	0.383	0.335
Rapamycin	0.491	0.365
Tcell	0.16	0.235
GMCSF	-0.417	0.848
IFNab	0.076	0.596
IFNg	0.053	-0.032
IFNg_GMCSF1	-0.242	0.321
Rv1432_day32	0.18	0.194
Rv1565c_day32	0.0	0.573
secA2_input	1.014	-0.441
delta_Rv3594	0.333	0.0
delta_Rv3717	0.313	-0.361
delta_Rv3811	0.744	-0.089
delta_Rv0954	-0.37	0.315
PonA1	-0.247	-1.182
EccD1_KO	-0.312	-0.543
EspI_KO	-0.111	-0.137
PE35_KO	0.545	-0.16
PPE68_KO	-0.797	-0.406
glycerol2	0.722	0.808
lignocerate	0.781	0.591
oleate	0.98	0.591
phosphatidylcholine	0.79	0.616
acetate	0.617	0.258
glucAc	0.333	0.116
Rv0950ko	-0.054	-0.066
Rv1096ko	0.573	-0.371
Rv3684ko	-0.16	0.072
delta_otsA_trehalose	0.07	-0.238