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 Rv0778/cyp126

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

	Rv3104c/-	Rv0778/cyp126
Fe_supp_jason_reseq	1.44	2.014
low_pH_jason_reseq	-0.574	-0.571
NO_jason_reseq	-0.704	-0.651
B6_jason_reseq	-0.434	0.523
MHCII_jason_reseq	0.884	0.706
Isoniazid02	0.127	-0.525
Rifampicin4	0.192	0.157
Ethambutol3	-0.592	-0.403
Meropenem3	0.458	0.298
Vancomycin16	-0.175	0.154
Rv2680_day32	-0.354	0.508
H37Rv_KO_MarP	0.765	-0.423
hypoxia_3wks	1.188	0.534
hypoxia_6wks	1.566	-0.021
glycerol	0.278	0.736
cholesterol	-0.34	0.449
AJ	-0.445	0.824
Bibs02	-0.16	0.174
Bibs02c	-0.42	0.246
BL6	0.101	-0.148
BL6a	0.344	0.756
BXD01	0.493	0.734
BXD010	0.367	0.959
BXD011	0.358	0.899
BXD03	0.073	0.561
BXD04	1.237	1.184
BXD05	1.169	0.862
BXD06	0.24	0.836
BXD07	0.855	0.79
BXD08	0.73	0.618
BXD09	0.447	0.696
CAST	-0.384	0.756
CCcont	0.608	-0.056
DS01	-0.226	0.921
DS02	0.287	1.078
DS04	-0.829	0.207
DS0c	0.679	0.919
GP01	-0.313	-0.265
GP02	-0.321	-0.021
GP0c	0.359	0.665
NOD	0.905	1.642
NZO	0.027	0.581
PWK	0.081	0.715
H37Rv_KO_CtpC	0.723	0.916
H37Rv_KO_CtpD	1.029	1.194
H37Rv_KO_Rv1272	-0.168	-0.269
H37Rv_KO_SugABC	0.33	1.345
H37Rv_KO_MbtN	0.11	0.918
Trans05	0.131	0.278
macrophage_unactivated	0.464	1.042
IL1	0.768	0.0
Rapamycin	1.467	0.341
Tcell	0.652	0.437
GMCSF	0.409	0.591
IFNab	0.348	0.0
IFNg	0.35	1.04
IFNg_GMCSF1	0.606	0.566
Rv1432_day32	0.789	-0.624
Rv1565c_day32	-1.671	-0.347
secA2_input	0.611	0.23
delta_Rv3594	0.211	0.72
delta_Rv3717	0.0	-0.162
delta_Rv3811	-0.126	0.744
delta_Rv0954	0.981	0.549
PonA1	0.233	0.753
EccD1_KO	-0.927	0.52
EspI_KO	0.063	0.893
PE35_KO	-0.747	0.983
PPE68_KO	-0.682	0.841
glycerol2	-0.46	-0.13
lignocerate	-0.342	-0.614
oleate	-0.323	0.39
phosphatidylcholine	-0.287	0.088
acetate	-0.642	-0.748
glucAc	-0.365	-1.202
Rv0950ko	0.582	0.329
Rv1096ko	0.431	0.633
Rv3684ko	0.422	0.121
delta_otsA_trehalose	-1.37	-1.184