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 Rv2044c/-

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

	Rv1990A/-	Rv2044c/-
Fe_supp_jason_reseq	0.0	-0.147
low_pH_jason_reseq	-0.664	-0.069
NO_jason_reseq	0.189	0.129
B6_jason_reseq	-1.972	-1.201
MHCII_jason_reseq	-1.757	-0.938
Isoniazid02	3.843	-0.017
Rifampicin4	0.344	0.477
Ethambutol3	0.426	-0.261
Meropenem3	-0.214	0.559
Vancomycin16	0.109	0.414
Rv2680_day32	-2.044	0.368
H37Rv_KO_MarP	0.234	0.507
hypoxia_3wks	0.156	0.805
hypoxia_6wks	-0.013	0.507
glycerol	-0.524	-1.391
cholesterol	-1.205	-1.771
AJ	-0.718	-1.025
Bibs02	-3.247	-2.035
Bibs02c	-1.288	-0.812
BL6	0.304	0.394
BL6a	0.522	0.11
BXD01	1.7	0.561
BXD010	1.82	1.129
BXD011	0.735	0.631
BXD03	0.678	0.448
BXD04	0.62	0.018
BXD05	1.24	0.805
BXD06	0.582	0.569
BXD07	1.093	0.932
BXD08	0.602	0.44
BXD09	0.977	0.734
CAST	-0.415	0.48
CCcont	0.528	0.6
DS01	0.202	0.051
DS02	-0.729	-1.188
DS04	-1.876	-1.448
DS0c	0.198	0.251
GP01	-0.48	-0.551
GP02	1.816	0.431
GP0c	0.506	-0.17
NOD	1.196	2.28
NZO	-1.37	-0.029
PWK	-0.728	-0.911
H37Rv_KO_CtpC	1.267	1.245
H37Rv_KO_CtpD	-0.307	1.427
H37Rv_KO_Rv1272	0.905	0.208
H37Rv_KO_SugABC	1.82	0.547
H37Rv_KO_MbtN	-0.511	0.52
Trans05	1.228	0.168
macrophage_unactivated	1.701	0.688
IL1	0.383	-0.172
Rapamycin	0.491	0.531
Tcell	0.16	0.124
GMCSF	-0.417	0.589
IFNab	0.076	0.641
IFNg	0.053	0.553
IFNg_GMCSF1	-0.242	-0.141
Rv1432_day32	0.18	3.684
Rv1565c_day32	0.0	0.25
secA2_input	1.014	-1.127
delta_Rv3594	0.333	0.881
delta_Rv3717	0.313	0.253
delta_Rv3811	0.744	0.62
delta_Rv0954	-0.37	0.895
PonA1	-0.247	-0.33
EccD1_KO	-0.312	-0.789
EspI_KO	-0.111	-0.177
PE35_KO	0.545	0.158
PPE68_KO	-0.797	0.438
glycerol2	0.722	0.513
lignocerate	0.781	0.256
oleate	0.98	0.586
phosphatidylcholine	0.79	0.382
acetate	0.617	-0.407
glucAc	0.333	0.217
Rv0950ko	-0.054	0.531
Rv1096ko	0.573	0.739
Rv3684ko	-0.16	-0.121
delta_otsA_trehalose	0.07	0.901