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 Rv0463/-:

update plot	correlation	link to info on gene
Rv2833c/ugpB	(cc=0.5193)	info on Rv2833c/ugpB
Rv1931c/-	(cc=0.5052)	info on Rv1931c/-
Rv2151c/ftsQ	(cc=0.4516)	info on Rv2151c/ftsQ
Rv2251/-	(cc=0.4489)	info on Rv2251/-
Rv1574/-	(cc=0.4478)	info on Rv1574/-
Rv2620c/-	(cc=0.4382)	info on Rv2620c/-
Rv0318c/-	(cc=0.4317)	info on Rv0318c/-
Rv0494/-	(cc=0.4242)	info on Rv0494/-
Rv0728c/serA2	(cc=0.4207)	info on Rv0728c/serA2
Rv2970A/-	(cc=0.4164)	info on Rv2970A/-

Correlation of Rv0463/- with Rv0728c/serA2

Normalized LFCs for Rv0463/-:
(description and provenance of datasets)

	Rv0463/-	Rv0728c/serA2
Fe_supp_jason_reseq	-0.008	0.584
low_pH_jason_reseq	-0.403	-0.744
NO_jason_reseq	-0.677	-0.494
B6_jason_reseq	-1.18	-0.184
MHCII_jason_reseq	-1.029	-0.151
Isoniazid02	0.274	0.068
Rifampicin4	0.246	0.349
Ethambutol3	0.507	0.0
Meropenem3	1.163	1.656
Vancomycin16	0.992	0.822
Rv2680_day32	0.272	-0.252
H37Rv_KO_MarP	0.612	0.246
hypoxia_3wks	-0.666	0.387
hypoxia_6wks	-0.15	0.679
glycerol	-0.413	-0.471
cholesterol	-1.723	-0.371
AJ	-1.213	0.282
Bibs02	0.762	-0.832
Bibs02c	1.006	0.42
BL6	0.576	0.407
BL6a	0.428	0.336
BXD01	0.418	0.242
BXD010	-0.866	0.989
BXD011	0.7	1.865
BXD03	-0.718	0.127
BXD04	0.113	0.472
BXD05	0.048	0.818
BXD06	-0.146	0.666
BXD07	0.137	0.462
BXD08	0.201	0.752
BXD09	0.128	0.624
CAST	-0.022	0.342
CCcont	1.167	-0.076
DS01	-0.2	-0.26
DS02	0.124	-0.969
DS04	-1.698	-0.707
DS0c	-1.103	-0.625
GP01	-1.374	-0.703
GP02	-1.038	-1.195
GP0c	-0.652	-0.776
NOD	-1.077	-0.456
NZO	0.416	0.538
PWK	-0.091	-0.151
H37Rv_KO_CtpC	0.014	0.896
H37Rv_KO_CtpD	-0.982	-1.949
H37Rv_KO_Rv1272	-0.169	0.626
H37Rv_KO_SugABC	-1.953	0.361
H37Rv_KO_MbtN	-0.343	0.712
Trans05	1.108	0.327
macrophage_unactivated	0.565	0.0
IL1	1.026	0.056
Rapamycin	0.654	0.678
Tcell	1.144	0.244
GMCSF	1.141	0.116
IFNab	1.022	0.0
IFNg	1.053	0.361
IFNg_GMCSF1	0.305	0.71
Rv1432_day32	-0.43	1.709
Rv1565c_day32	-0.144	0.392
secA2_input	-0.601	0.044
delta_Rv3594	-1.196	-1.418
delta_Rv3717	-1.763	-0.603
delta_Rv3811	-0.971	-0.931
delta_Rv0954	-0.994	-0.848
PonA1	-1.825	0.07
EccD1_KO	-0.335	0.026
EspI_KO	0.927	0.242
PE35_KO	0.808	-0.166
PPE68_KO	0.064	-0.624
glycerol2	0.977	0.242
lignocerate	0.718	0.407
oleate	0.217	0.047
phosphatidylcholine	0.462	0.113
acetate	0.903	-0.113
glucAc	0.123	0.116
Rv0950ko	1.309	0.078
Rv1096ko	0.214	-0.133
Rv3684ko	-0.449	-0.413
delta_otsA_trehalose	-1.296	-0.68