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 Rv3857c/-

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

	Rv3104c/-	Rv3857c/-
Fe_supp_jason_reseq	1.44	0.483
low_pH_jason_reseq	-0.574	-0.313
NO_jason_reseq	-0.704	-0.11
B6_jason_reseq	-0.434	-0.528
MHCII_jason_reseq	0.884	-0.032
Isoniazid02	0.127	0.258
Rifampicin4	0.192	0.368
Ethambutol3	-0.592	-0.074
Meropenem3	0.458	1.325
Vancomycin16	-0.175	0.371
Rv2680_day32	-0.354	-0.66
H37Rv_KO_MarP	0.765	0.15
hypoxia_3wks	1.188	0.076
hypoxia_6wks	1.566	0.714
glycerol	0.278	0.622
cholesterol	-0.34	0.186
AJ	-0.445	0.163
Bibs02	-0.16	0.114
Bibs02c	-0.42	1.507
BL6	0.101	-0.02
BL6a	0.344	1.478
BXD01	0.493	0.741
BXD010	0.367	1.076
BXD011	0.358	0.564
BXD03	0.073	0.506
BXD04	1.237	0.98
BXD05	1.169	0.211
BXD06	0.24	0.209
BXD07	0.855	0.458
BXD08	0.73	-0.271
BXD09	0.447	0.354
CAST	-0.384	-0.028
CCcont	0.608	0.516
DS01	-0.226	1.081
DS02	0.287	1.875
DS04	-0.829	0.943
DS0c	0.679	0.842
GP01	-0.313	-0.824
GP02	-0.321	0.684
GP0c	0.359	-0.115
NOD	0.905	2.579
NZO	0.027	-0.779
PWK	0.081	1.708
H37Rv_KO_CtpC	0.723	-0.634
H37Rv_KO_CtpD	1.029	1.678
H37Rv_KO_Rv1272	-0.168	1.285
H37Rv_KO_SugABC	0.33	1.318
H37Rv_KO_MbtN	0.11	1.061
Trans05	0.131	0.668
macrophage_unactivated	0.464	0.139
IL1	0.768	0.101
Rapamycin	1.467	-0.595
Tcell	0.652	0.326
GMCSF	0.409	-0.919
IFNab	0.348	-0.166
IFNg	0.35	-0.593
IFNg_GMCSF1	0.606	-0.487
Rv1432_day32	0.789	1.901
Rv1565c_day32	-1.671	-5.489
secA2_input	0.611	-1.11
delta_Rv3594	0.211	-1.072
delta_Rv3717	0.0	-1.645
delta_Rv3811	-0.126	-1.216
delta_Rv0954	0.981	-0.478
PonA1	0.233	-0.461
EccD1_KO	-0.927	-0.506
EspI_KO	0.063	-2.099
PE35_KO	-0.747	-0.942
PPE68_KO	-0.682	-2.073
glycerol2	-0.46	-0.915
lignocerate	-0.342	-1.059
oleate	-0.323	-1.018
phosphatidylcholine	-0.287	-1.335
acetate	-0.642	-2.051
glucAc	-0.365	-1.108
Rv0950ko	0.582	-0.133
Rv1096ko	0.431	0.305
Rv3684ko	0.422	1.562
delta_otsA_trehalose	-1.37	-0.173