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 Rv0380c/-

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

	Rv3104c/-	Rv0380c/-
Fe_supp_jason_reseq	1.44	-0.688
low_pH_jason_reseq	-0.574	-0.42
NO_jason_reseq	-0.704	0.16
B6_jason_reseq	-0.434	-0.516
MHCII_jason_reseq	0.884	-2.249
Isoniazid02	0.127	-0.534
Rifampicin4	0.192	0.983
Ethambutol3	-0.592	-0.111
Meropenem3	0.458	-0.072
Vancomycin16	-0.175	0.512
Rv2680_day32	-0.354	-1.968
H37Rv_KO_MarP	0.765	0.576
hypoxia_3wks	1.188	2.333
hypoxia_6wks	1.566	0.123
glycerol	0.278	-1.934
cholesterol	-0.34	-0.904
AJ	-0.445	-0.393
Bibs02	-0.16	-0.976
Bibs02c	-0.42	-2.822
BL6	0.101	-0.467
BL6a	0.344	-0.106
BXD01	0.493	0.0
BXD010	0.367	1.448
BXD011	0.358	0.495
BXD03	0.073	1.529
BXD04	1.237	0.705
BXD05	1.169	1.603
BXD06	0.24	0.895
BXD07	0.855	0.768
BXD08	0.73	0.674
BXD09	0.447	0.962
CAST	-0.384	-0.946
CCcont	0.608	0.379
DS01	-0.226	-0.4
DS02	0.287	-1.815
DS04	-0.829	-2.129
DS0c	0.679	-0.058
GP01	-0.313	-0.617
GP02	-0.321	-0.744
GP0c	0.359	-0.105
NOD	0.905	-1.403
NZO	0.027	-1.153
PWK	0.081	-1.637
H37Rv_KO_CtpC	0.723	-0.275
H37Rv_KO_CtpD	1.029	-1.39
H37Rv_KO_Rv1272	-0.168	-0.526
H37Rv_KO_SugABC	0.33	-0.885
H37Rv_KO_MbtN	0.11	-1.056
Trans05	0.131	-0.816
macrophage_unactivated	0.464	0.306
IL1	0.768	2.005
Rapamycin	1.467	0.298
Tcell	0.652	1.153
GMCSF	0.409	1.096
IFNab	0.348	0.671
IFNg	0.35	2.189
IFNg_GMCSF1	0.606	1.797
Rv1432_day32	0.789	0.769
Rv1565c_day32	-1.671	-1.106
secA2_input	0.611	0.725
delta_Rv3594	0.211	1.484
delta_Rv3717	0.0	1.221
delta_Rv3811	-0.126	1.616
delta_Rv0954	0.981	0.149
PonA1	0.233	1.898
EccD1_KO	-0.927	-1.519
EspI_KO	0.063	-3.026
PE35_KO	-0.747	-2.532
PPE68_KO	-0.682	-2.662
glycerol2	-0.46	-0.856
lignocerate	-0.342	-0.794
oleate	-0.323	-0.037
phosphatidylcholine	-0.287	-0.545
acetate	-0.642	-1.084
glucAc	-0.365	-0.474
Rv0950ko	0.582	0.552
Rv1096ko	0.431	1.725
Rv3684ko	0.422	1.326
delta_otsA_trehalose	-1.37	0.111