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 Rv3517/-:

update plot	correlation	link to info on gene
Rv3694c/-	(cc=0.4981)	info on Rv3694c/-
Rv3689/-	(cc=0.4812)	info on Rv3689/-
Rv3796/-	(cc=0.4794)	info on Rv3796/-
Rv2253/-	(cc=0.4682)	info on Rv2253/-
Rv0831c/-	(cc=0.463)	info on Rv0831c/-
Rv3744/nmtR	(cc=0.4522)	info on Rv3744/nmtR
Rv3695/-	(cc=0.4453)	info on Rv3695/-
Rv1585c/-	(cc=0.4422)	info on Rv1585c/-
Rv3142c/-	(cc=0.4388)	info on Rv3142c/-
Rv3378c/-	(cc=0.4266)	info on Rv3378c/-

Correlation of Rv3517/- with Rv3689/-

Normalized LFCs for Rv3517/-:
(description and provenance of datasets)

	Rv3517/-	Rv3689/-
Fe_supp_jason_reseq	0.3	-0.388
low_pH_jason_reseq	-1.491	-1.681
NO_jason_reseq	-0.541	0.105
B6_jason_reseq	-0.856	0.499
MHCII_jason_reseq	-0.266	-0.62
Isoniazid02	-0.419	-1.107
Rifampicin4	0.65	0.495
Ethambutol3	0.514	0.951
Meropenem3	1.004	-0.364
Vancomycin16	-0.297	-0.058
Rv2680_day32	-0.576	-0.811
H37Rv_KO_MarP	0.016	-1.24
hypoxia_3wks	-0.427	0.638
hypoxia_6wks	-0.397	0.739
glycerol	-0.793	-0.295
cholesterol	0.252	-0.2
AJ	1.592	0.576
Bibs02	0.736	-0.311
Bibs02c	0.202	-0.073
BL6	0.556	0.728
BL6a	-0.076	0.844
BXD01	0.731	1.055
BXD010	0.671	0.8
BXD011	0.3	0.852
BXD03	0.891	1.454
BXD04	0.279	1.548
BXD05	0.234	1.047
BXD06	0.218	0.962
BXD07	0.084	1.026
BXD08	1.061	1.004
BXD09	0.589	0.486
CAST	0.14	1.677
CCcont	0.639	0.27
DS01	0.869	-0.202
DS02	0.354	0.044
DS04	1.117	0.225
DS0c	0.08	-0.091
GP01	0.805	0.821
GP02	-0.124	0.096
GP0c	1.021	0.85
NOD	1.778	0.957
NZO	0.803	1.16
PWK	1.833	2.364
H37Rv_KO_CtpC	1.432	0.806
H37Rv_KO_CtpD	0.683	0.981
H37Rv_KO_Rv1272	1.625	0.967
H37Rv_KO_SugABC	0.39	1.067
H37Rv_KO_MbtN	-0.153	1.472
Trans05	1.08	0.496
macrophage_unactivated	0.698	0.079
IL1	0.036	-0.374
Rapamycin	-0.629	-0.997
Tcell	0.948	0.508
GMCSF	0.063	0.132
IFNab	0.245	0.206
IFNg	-0.265	0.722
IFNg_GMCSF1	0.327	0.452
Rv1432_day32	-0.394	1.172
Rv1565c_day32	-0.357	-0.482
secA2_input	0.332	-0.488
delta_Rv3594	-0.408	-0.58
delta_Rv3717	-0.258	-0.205
delta_Rv3811	0.016	-0.21
delta_Rv0954	-0.362	-0.979
PonA1	1.154	-0.099
EccD1_KO	0.766	0.122
EspI_KO	-0.439	-0.217
PE35_KO	0.055	0.295
PPE68_KO	0.358	0.208
glycerol2	0.611	0.27
lignocerate	0.746	-0.029
oleate	0.956	0.717
phosphatidylcholine	0.728	-0.052
acetate	0.12	0.284
glucAc	0.223	0.188
Rv0950ko	0.036	0.202
Rv1096ko	1.616	0.85
Rv3684ko	1.33	0.799
delta_otsA_trehalose	0.831	-0.482