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 Rv1533/-

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

	Rv3104c/-	Rv1533/-
Fe_supp_jason_reseq	1.44	0.369
low_pH_jason_reseq	-0.574	-0.532
NO_jason_reseq	-0.704	-0.683
B6_jason_reseq	-0.434	0.119
MHCII_jason_reseq	0.884	0.458
Isoniazid02	0.127	-0.212
Rifampicin4	0.192	-0.233
Ethambutol3	-0.592	0.114
Meropenem3	0.458	-0.612
Vancomycin16	-0.175	-0.512
Rv2680_day32	-0.354	0.272
H37Rv_KO_MarP	0.765	0.068
hypoxia_3wks	1.188	0.63
hypoxia_6wks	1.566	1.253
glycerol	0.278	0.607
cholesterol	-0.34	0.106
AJ	-0.445	0.17
Bibs02	-0.16	0.054
Bibs02c	-0.42	0.605
BL6	0.101	0.797
BL6a	0.344	1.093
BXD01	0.493	0.944
BXD010	0.367	-0.21
BXD011	0.358	1.169
BXD03	0.073	0.647
BXD04	1.237	1.188
BXD05	1.169	1.156
BXD06	0.24	1.322
BXD07	0.855	0.537
BXD08	0.73	0.792
BXD09	0.447	0.658
CAST	-0.384	-0.377
CCcont	0.608	1.47
DS01	-0.226	0.303
DS02	0.287	0.249
DS04	-0.829	0.0
DS0c	0.679	0.952
GP01	-0.313	1.233
GP02	-0.321	0.51
GP0c	0.359	0.218
NOD	0.905	0.067
NZO	0.027	0.577
PWK	0.081	0.277
H37Rv_KO_CtpC	0.723	0.293
H37Rv_KO_CtpD	1.029	1.396
H37Rv_KO_Rv1272	-0.168	0.674
H37Rv_KO_SugABC	0.33	1.739
H37Rv_KO_MbtN	0.11	1.062
Trans05	0.131	1.248
macrophage_unactivated	0.464	0.657
IL1	0.768	0.252
Rapamycin	1.467	0.295
Tcell	0.652	0.782
GMCSF	0.409	0.491
IFNab	0.348	-0.076
IFNg	0.35	0.131
IFNg_GMCSF1	0.606	-0.16
Rv1432_day32	0.789	-0.674
Rv1565c_day32	-1.671	0.174
secA2_input	0.611	1.207
delta_Rv3594	0.211	0.128
delta_Rv3717	0.0	0.763
delta_Rv3811	-0.126	0.062
delta_Rv0954	0.981	0.671
PonA1	0.233	1.589
EccD1_KO	-0.927	-1.125
EspI_KO	0.063	-1.705
PE35_KO	-0.747	-0.948
PPE68_KO	-0.682	-0.989
glycerol2	-0.46	0.31
lignocerate	-0.342	0.395
oleate	-0.323	0.143
phosphatidylcholine	-0.287	0.637
acetate	-0.642	0.284
glucAc	-0.365	0.212
Rv0950ko	0.582	0.103
Rv1096ko	0.431	0.305
Rv3684ko	0.422	0.832
delta_otsA_trehalose	-1.37	-0.898