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 Rv3695/-

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

	Rv3517/-	Rv3695/-
Fe_supp_jason_reseq	0.3	-0.86
low_pH_jason_reseq	-1.491	-2.494
NO_jason_reseq	-0.541	-1.788
B6_jason_reseq	-0.856	-1.093
MHCII_jason_reseq	-0.266	-0.8
Isoniazid02	-0.419	-0.787
Rifampicin4	0.65	0.119
Ethambutol3	0.514	0.829
Meropenem3	1.004	0.603
Vancomycin16	-0.297	0.194
Rv2680_day32	-0.576	-0.154
H37Rv_KO_MarP	0.016	-1.541
hypoxia_3wks	-0.427	0.163
hypoxia_6wks	-0.397	0.572
glycerol	-0.793	-1.725
cholesterol	0.252	-0.747
AJ	1.592	0.993
Bibs02	0.736	-0.384
Bibs02c	0.202	1.558
BL6	0.556	1.26
BL6a	-0.076	1.501
BXD01	0.731	0.908
BXD010	0.671	0.548
BXD011	0.3	-0.332
BXD03	0.891	1.2
BXD04	0.279	0.945
BXD05	0.234	0.67
BXD06	0.218	0.351
BXD07	0.084	0.568
BXD08	1.061	0.186
BXD09	0.589	0.277
CAST	0.14	0.859
CCcont	0.639	0.793
DS01	0.869	-0.7
DS02	0.354	-1.122
DS04	1.117	0.849
DS0c	0.08	-0.933
GP01	0.805	1.207
GP02	-0.124	0.442
GP0c	1.021	1.297
NOD	1.778	-0.625
NZO	0.803	1.348
PWK	1.833	2.835
H37Rv_KO_CtpC	1.432	1.252
H37Rv_KO_CtpD	0.683	-0.398
H37Rv_KO_Rv1272	1.625	0.146
H37Rv_KO_SugABC	0.39	1.541
H37Rv_KO_MbtN	-0.153	1.843
Trans05	1.08	-0.703
macrophage_unactivated	0.698	-0.382
IL1	0.036	0.184
Rapamycin	-0.629	-0.479
Tcell	0.948	-0.212
GMCSF	0.063	-0.084
IFNab	0.245	1.584
IFNg	-0.265	0.192
IFNg_GMCSF1	0.327	0.842
Rv1432_day32	-0.394	-0.819
Rv1565c_day32	-0.357	-0.746
secA2_input	0.332	-2.552
delta_Rv3594	-0.408	1.231
delta_Rv3717	-0.258	0.714
delta_Rv3811	0.016	0.526
delta_Rv0954	-0.362	0.18
PonA1	1.154	1.809
EccD1_KO	0.766	1.02
EspI_KO	-0.439	-0.245
PE35_KO	0.055	0.236
PPE68_KO	0.358	0.506
glycerol2	0.611	-1.103
lignocerate	0.746	-0.306
oleate	0.956	0.839
phosphatidylcholine	0.728	-0.496
acetate	0.12	0.068
glucAc	0.223	-0.089
Rv0950ko	0.036	0.582
Rv1096ko	1.616	1.99
Rv3684ko	1.33	2.109
delta_otsA_trehalose	0.831	-0.457