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 Rv1458c/-:

update plot	correlation	link to info on gene
Rv1457c/-	(cc=0.6697)	info on Rv1457c/-
Rv3043c/ctaD	(cc=0.6387)	info on Rv3043c/ctaD
Rv2202c/adoK	(cc=0.532)	info on Rv2202c/adoK
Rv2965c/kdtB	(cc=0.5109)	info on Rv2965c/kdtB
Rv0651/rplJ	(cc=0.5061)	info on Rv0651/rplJ
Rv1636/TB15.3	(cc=0.5061)	info on Rv1636/TB15.3
Rv0244c/fadE5	(cc=0.4986)	info on Rv0244c/fadE5
Rv1845c/blaR	(cc=0.4975)	info on Rv1845c/blaR
Rv3274c/fadE25	(cc=0.4882)	info on Rv3274c/fadE25
Rv0455c/-	(cc=0.4814)	info on Rv0455c/-

Correlation of Rv1458c/- with Rv0455c/-

Normalized LFCs for Rv1458c/-:
(description and provenance of datasets)

	Rv1458c/-	Rv0455c/-
Fe_supp_jason_reseq	1.209	3.939
low_pH_jason_reseq	0.811	0.211
NO_jason_reseq	0.0	-0.362
B6_jason_reseq	0.0	-0.153
MHCII_jason_reseq	0.0	-0.135
Isoniazid02	-0.383	0.167
Rifampicin4	-0.712	-0.341
Ethambutol3	0.612	0.27
Meropenem3	1.402	0.0
Vancomycin16	0.0	-0.334
Rv2680_day32	-0.131	0.0
H37Rv_KO_MarP	1.946	4.219
hypoxia_3wks	0.0	-1.511
hypoxia_6wks	0.0	-0.791
glycerol	0.554	0.0
cholesterol	0.398	0.0
AJ	0.0	0.0
Bibs02	0.0	0.0
Bibs02c	0.0	0.0
BL6	0.0	0.0
BL6a	0.0	0.0
BXD01	0.0	0.0
BXD010	0.0	0.0
BXD011	0.127	0.54
BXD03	0.0	0.0
BXD04	0.0	0.0
BXD05	0.0	0.0
BXD06	0.0	0.0
BXD07	0.0	0.0
BXD08	0.0	0.0
BXD09	0.0	0.0
CAST	0.0	0.0
CCcont	0.149	2.716
DS01	0.0	0.0
DS02	0.217	0.0
DS04	0.0	0.37
DS0c	0.0	0.0
GP01	0.0	0.0
GP02	0.0	0.0
GP0c	0.0	0.0
NOD	0.0	0.0
NZO	0.0	0.0
PWK	0.0	0.0
H37Rv_KO_CtpC	0.446	0.0
H37Rv_KO_CtpD	0.85	0.445
H37Rv_KO_Rv1272	0.0	0.0
H37Rv_KO_SugABC	0.099	0.189
H37Rv_KO_MbtN	0.0	0.103
Trans05	0.0	0.131
macrophage_unactivated	0.0	0.0
IL1	0.0	0.0
Rapamycin	0.0	0.0
Tcell	0.0	0.0
GMCSF	0.0	0.0
IFNab	0.0	0.0
IFNg	0.0	0.0
IFNg_GMCSF1	0.0	0.0
Rv1432_day32	0.0	0.0
Rv1565c_day32	0.0	0.0
secA2_input	2.602	1.273
delta_Rv3594	-1.014	-1.597
delta_Rv3717	-0.688	-0.143
delta_Rv3811	-0.656	-1.423
delta_Rv0954	0.788	-2.762
PonA1	-0.286	-3.142
EccD1_KO	-1.273	-0.595
EspI_KO	0.234	-1.435
PE35_KO	-0.254	1.085
PPE68_KO	-0.278	0.0
glycerol2	-0.68	0.0
lignocerate	-0.591	0.0
oleate	-0.688	0.0
phosphatidylcholine	-0.679	0.0
acetate	-0.806	0.0
glucAc	0.103	0.0
Rv0950ko	-0.582	-3.169
Rv1096ko	-0.582	-2.868
Rv3684ko	-0.632	-4.169
delta_otsA_trehalose	-1.007	0.0