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 Rv3002c/ilvN:

update plot	correlation	link to info on gene
Rv2956/-	(cc=0.4482)	info on Rv2956/-
Rv0531/-	(cc=0.4354)	info on Rv0531/-
Rv2690c/-	(cc=0.3855)	info on Rv2690c/-
Rv1512/epiA	(cc=0.3578)	info on Rv1512/epiA
Rv3102c/ftsE	(cc=0.3569)	info on Rv3102c/ftsE
Rv2174/mptA	(cc=0.3524)	info on Rv2174/mptA
Rv1114/vapC32	(cc=0.3497)	info on Rv1114/vapC32
Rv2798c/-	(cc=0.3438)	info on Rv2798c/-
Rv1872c/lldD2	(cc=0.3273)	info on Rv1872c/lldD2
Rv2221c/glnE	(cc=0.3259)	info on Rv2221c/glnE

Correlation of Rv3002c/ilvN with Rv2690c/-

Normalized LFCs for Rv3002c/ilvN:
(description and provenance of datasets)

	Rv3002c/ilvN	Rv2690c/-
Fe_supp_jason_reseq	1.339	0.0
low_pH_jason_reseq	0.0	0.0
NO_jason_reseq	0.0	0.0
B6_jason_reseq	0.0	0.0
MHCII_jason_reseq	0.257	0.0
Isoniazid02	-0.183	0.437
Rifampicin4	0.0	1.681
Ethambutol3	0.0	0.251
Meropenem3	0.497	0.562
Vancomycin16	1.101	2.502
Rv2680_day32	0.0	-0.249
H37Rv_KO_MarP	-1.197	-1.317
hypoxia_3wks	0.55	0.0
hypoxia_6wks	0.0	0.0
glycerol	-0.202	0.0
cholesterol	-0.145	1.663
AJ	-0.232	0.0
Bibs02	-0.183	0.0
Bibs02c	-0.209	0.0
BL6	-0.125	0.0
BL6a	0.181	0.0
BXD01	0.227	0.0
BXD010	0.224	0.0
BXD011	-0.127	0.0
BXD03	2.111	0.0
BXD04	-0.124	0.0
BXD05	0.0	0.0
BXD06	0.122	0.0
BXD07	0.126	0.0
BXD08	0.0	0.0
BXD09	-0.14	0.0
CAST	-0.23	0.0
CCcont	-0.149	0.285
DS01	-0.236	0.0
DS02	-0.217	0.0
DS04	0.489	0.533
DS0c	-0.217	0.0
GP01	-0.099	0.0
GP02	-0.083	0.0
GP0c	-0.13	0.0
NOD	-0.225	0.0
NZO	-0.199	0.0
PWK	-0.196	0.0
H37Rv_KO_CtpC	-0.162	0.162
H37Rv_KO_CtpD	-0.127	0.0
H37Rv_KO_Rv1272	-0.141	0.0
H37Rv_KO_SugABC	0.451	1.783
H37Rv_KO_MbtN	-0.103	0.283
Trans05	-0.131	0.0
macrophage_unactivated	0.0	0.0
IL1	-0.374	0.0
Rapamycin	-0.387	0.0
Tcell	-0.857	0.0
GMCSF	-0.333	0.0
IFNab	0.973	0.0
IFNg	-0.703	0.0
IFNg_GMCSF1	0.0	0.0
Rv1432_day32	0.0	0.0
Rv1565c_day32	0.0	0.0
secA2_input	-0.412	-0.916
delta_Rv3594	0.402	1.086
delta_Rv3717	0.61	0.563
delta_Rv3811	1.139	1.282
delta_Rv0954	0.0	0.311
PonA1	0.0	0.145
EccD1_KO	1.542	-0.678
EspI_KO	-0.687	-0.918
PE35_KO	1.811	0.767
PPE68_KO	-0.771	0.298
glycerol2	0.0	0.0
lignocerate	0.0	0.0
oleate	0.0	0.0
phosphatidylcholine	0.0	0.0
acetate	0.0	0.0
glucAc	0.0	0.0
Rv0950ko	-0.482	-1.251
Rv1096ko	-0.483	0.262
Rv3684ko	-0.524	-0.982
delta_otsA_trehalose	0.0	-0.014