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 Rv3104c/-:

update plot	correlation	link to info on gene
Rv1128c/-	(cc=0.4738)	info on Rv1128c/-
Rv1752/-	(cc=0.4619)	info on Rv1752/-
Rv0778/cyp126	(cc=0.4422)	info on Rv0778/cyp126
Rv0587/yrbE2A	(cc=0.4378)	info on Rv0587/yrbE2A
Rv3857c/-	(cc=0.4356)	info on Rv3857c/-
Rv3779/-	(cc=0.4352)	info on Rv3779/-
Rv1533/-	(cc=0.434)	info on Rv1533/-
Rv2824c/-	(cc=0.4263)	info on Rv2824c/-
Rv0380c/-	(cc=0.4129)	info on Rv0380c/-
Rv0619/galTb	(cc=0.4119)	info on Rv0619/galTb

Correlation of Rv3104c/- with Rv0587/yrbE2A

Normalized LFCs for Rv3104c/-:
(description and provenance of datasets)

	Rv3104c/-	Rv0587/yrbE2A
Fe_supp_jason_reseq	1.44	1.25
low_pH_jason_reseq	-0.574	-1.016
NO_jason_reseq	-0.704	0.221
B6_jason_reseq	-0.434	0.735
MHCII_jason_reseq	0.884	0.082
Isoniazid02	0.127	0.02
Rifampicin4	0.192	-1.162
Ethambutol3	-0.592	-0.291
Meropenem3	0.458	-0.829
Vancomycin16	-0.175	-0.186
Rv2680_day32	-0.354	1.005
H37Rv_KO_MarP	0.765	0.404
hypoxia_3wks	1.188	0.786
hypoxia_6wks	1.566	1.714
glycerol	0.278	-0.051
cholesterol	-0.34	-0.651
AJ	-0.445	-0.089
Bibs02	-0.16	-0.558
Bibs02c	-0.42	0.912
BL6	0.101	1.175
BL6a	0.344	0.466
BXD01	0.493	0.976
BXD010	0.367	0.651
BXD011	0.358	1.845
BXD03	0.073	-0.531
BXD04	1.237	0.175
BXD05	1.169	0.458
BXD06	0.24	0.174
BXD07	0.855	0.497
BXD08	0.73	1.084
BXD09	0.447	0.302
CAST	-0.384	0.14
CCcont	0.608	-1.348
DS01	-0.226	-0.029
DS02	0.287	0.931
DS04	-0.829	-1.871
DS0c	0.679	1.068
GP01	-0.313	0.876
GP02	-0.321	-0.342
GP0c	0.359	1.175
NOD	0.905	-0.4
NZO	0.027	0.049
PWK	0.081	0.119
H37Rv_KO_CtpC	0.723	1.663
H37Rv_KO_CtpD	1.029	-0.304
H37Rv_KO_Rv1272	-0.168	0.579
H37Rv_KO_SugABC	0.33	-0.147
H37Rv_KO_MbtN	0.11	0.652
Trans05	0.131	-0.377
macrophage_unactivated	0.464	2.506
IL1	0.768	0.445
Rapamycin	1.467	0.933
Tcell	0.652	1.166
GMCSF	0.409	-0.578
IFNab	0.348	-0.209
IFNg	0.35	1.002
IFNg_GMCSF1	0.606	-0.446
Rv1432_day32	0.789	0.0
Rv1565c_day32	-1.671	1.006
secA2_input	0.611	-1.136
delta_Rv3594	0.211	-0.323
delta_Rv3717	0.0	-0.988
delta_Rv3811	-0.126	-1.261
delta_Rv0954	0.981	0.686
PonA1	0.233	0.384
EccD1_KO	-0.927	-0.855
EspI_KO	0.063	-0.291
PE35_KO	-0.747	-1.17
PPE68_KO	-0.682	-1.283
glycerol2	-0.46	-0.82
lignocerate	-0.342	-1.357
oleate	-0.323	0.444
phosphatidylcholine	-0.287	-0.581
acetate	-0.642	-1.699
glucAc	-0.365	-2.023
Rv0950ko	0.582	1.04
Rv1096ko	0.431	0.603
Rv3684ko	0.422	0.763
delta_otsA_trehalose	-1.37	-1.253