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 Rv3519/-:

update plot	correlation	link to info on gene
Rv0990c/-	(cc=0.5039)	info on Rv0990c/-
Rv3069/-	(cc=0.4877)	info on Rv3069/-
Rv2980/-	(cc=0.4589)	info on Rv2980/-
Rv2505c/fadD35	(cc=0.4514)	info on Rv2505c/fadD35
Rv1023/eno	(cc=0.4475)	info on Rv1023/eno
Rv1711/-	(cc=0.4393)	info on Rv1711/-
Rv1138c/-	(cc=0.4387)	info on Rv1138c/-
Rv1939/-	(cc=0.4269)	info on Rv1939/-
Rv2052c/-	(cc=0.4125)	info on Rv2052c/-
Rv3129/-	(cc=0.4061)	info on Rv3129/-

Correlation of Rv3519/- with Rv1023/eno

Normalized LFCs for Rv3519/-:
(description and provenance of datasets)

	Rv3519/-	Rv1023/eno
Fe_supp_jason_reseq	-0.436	0.415
low_pH_jason_reseq	0.03	0.0
NO_jason_reseq	0.803	0.0
B6_jason_reseq	0.639	0.0
MHCII_jason_reseq	0.692	0.0
Isoniazid02	-0.342	0.0
Rifampicin4	0.466	0.0
Ethambutol3	0.154	0.0
Meropenem3	-0.535	0.0
Vancomycin16	-0.271	0.0
Rv2680_day32	0.428	0.0
H37Rv_KO_MarP	-0.502	-0.71
hypoxia_3wks	-0.805	0.0
hypoxia_6wks	0.816	0.0
glycerol	0.295	0.0
cholesterol	-0.374	0.0
AJ	0.074	0.0
Bibs02	-0.073	0.0
Bibs02c	0.388	0.0
BL6	-0.12	0.0
BL6a	0.232	0.0
BXD01	-0.449	0.0
BXD010	-0.299	0.0
BXD011	-0.318	0.0
BXD03	-0.455	0.0
BXD04	0.159	0.0
BXD05	-0.857	0.0
BXD06	0.195	0.0
BXD07	-0.709	0.0
BXD08	-0.496	0.0
BXD09	0.063	0.0
CAST	-0.576	0.0
CCcont	-0.718	0.149
DS01	0.062	0.0
DS02	0.378	0.0
DS04	0.691	0.0
DS0c	0.793	0.0
GP01	0.505	0.0
GP02	0.862	0.0
GP0c	-0.017	0.0
NOD	-1.058	0.0
NZO	-1.27	0.0
PWK	-0.173	0.0
H37Rv_KO_CtpC	-0.392	0.0
H37Rv_KO_CtpD	0.683	0.0
H37Rv_KO_Rv1272	-0.284	0.0
H37Rv_KO_SugABC	0.038	0.0
H37Rv_KO_MbtN	0.915	0.0
Trans05	-0.009	0.0
macrophage_unactivated	0.148	0.0
IL1	0.833	0.0
Rapamycin	0.583	0.0
Tcell	0.753	0.0
GMCSF	0.333	0.0
IFNab	0.278	0.0
IFNg	0.278	0.0
IFNg_GMCSF1	-0.6	0.0
Rv1432_day32	-0.562	0.0
Rv1565c_day32	0.441	0.0
secA2_input	-0.225	-0.759
delta_Rv3594	-0.15	0.0
delta_Rv3717	-0.802	0.0
delta_Rv3811	-0.705	0.0
delta_Rv0954	-0.373	0.0
PonA1	-0.104	0.0
EccD1_KO	1.898	1.595
EspI_KO	2.002	1.934
PE35_KO	1.065	1.105
PPE68_KO	0.982	0.841
glycerol2	-0.383	0.0
lignocerate	-0.258	0.0
oleate	-0.267	0.0
phosphatidylcholine	-0.231	0.0
acetate	-0.07	0.0
glucAc	-0.363	0.0
Rv0950ko	0.38	0.0
Rv1096ko	1.348	-0.793
Rv3684ko	-0.236	-0.861
delta_otsA_trehalose	-0.576	0.0