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 Rv1669/-:

update plot	correlation	link to info on gene
Rv3839/-	(cc=0.444)	info on Rv3839/-
Rv2352c/PPE38	(cc=0.4404)	info on Rv2352c/PPE38
Rv3438/-	(cc=0.4334)	info on Rv3438/-
Rv2162c/PE_PGRS38	(cc=0.3833)	info on Rv2162c/PE_PGRS38
Rv2973c/recG	(cc=0.3768)	info on Rv2973c/recG
Rv1563c/treY	(cc=0.372)	info on Rv1563c/treY
Rv1562c/treZ	(cc=0.364)	info on Rv1562c/treZ
Rv0255c/cobQ1	(cc=0.3627)	info on Rv0255c/cobQ1
Rv0423c/thiC	(cc=0.3537)	info on Rv0423c/thiC
Rv3742c/-	(cc=0.3512)	info on Rv3742c/-

Correlation of Rv1669/- with Rv2973c/recG

Normalized LFCs for Rv1669/-:
(description and provenance of datasets)

	Rv1669/-	Rv2973c/recG
Fe_supp_jason_reseq	0.824	1.077
low_pH_jason_reseq	-0.519	-0.156
NO_jason_reseq	-1.756	0.155
B6_jason_reseq	0.0	1.006
MHCII_jason_reseq	-0.421	0.427
Isoniazid02	0.167	-0.031
Rifampicin4	-0.065	0.165
Ethambutol3	-0.153	0.536
Meropenem3	-0.151	0.253
Vancomycin16	0.804	-0.284
Rv2680_day32	0.633	0.228
H37Rv_KO_MarP	-0.601	-0.285
hypoxia_3wks	0.299	-0.443
hypoxia_6wks	-1.969	-0.549
glycerol	0.142	0.642
cholesterol	0.748	0.852
AJ	0.067	-0.225
Bibs02	-0.38	0.201
Bibs02c	1.391	0.555
BL6	-0.45	0.702
BL6a	0.821	0.63
BXD01	-0.204	0.248
BXD010	-0.137	0.429
BXD011	1.278	0.315
BXD03	-0.06	0.604
BXD04	0.0	0.136
BXD05	0.884	0.283
BXD06	0.677	0.202
BXD07	0.257	0.317
BXD08	-0.164	0.353
BXD09	0.407	0.494
CAST	0.591	-0.407
CCcont	0.164	1.099
DS01	1.09	1.194
DS02	-0.233	1.601
DS04	1.681	0.838
DS0c	0.267	0.69
GP01	-0.508	-1.067
GP02	0.547	0.092
GP0c	0.177	-0.507
NOD	0.576	0.384
NZO	0.621	0.178
PWK	0.524	0.216
H37Rv_KO_CtpC	-0.76	-0.475
H37Rv_KO_CtpD	0.173	0.192
H37Rv_KO_Rv1272	1.483	0.811
H37Rv_KO_SugABC	0.029	0.729
H37Rv_KO_MbtN	-0.214	-0.075
Trans05	1.157	0.584
macrophage_unactivated	1.035	-0.092
IL1	-0.042	-0.848
Rapamycin	-0.703	-0.773
Tcell	-0.433	-0.71
GMCSF	0.895	0.0
IFNab	0.33	0.493
IFNg	0.462	0.639
IFNg_GMCSF1	1.169	-0.28
Rv1432_day32	0.074	0.621
Rv1565c_day32	0.444	-0.142
secA2_input	-0.171	-0.276
delta_Rv3594	0.0	0.106
delta_Rv3717	-0.287	-0.045
delta_Rv3811	0.611	0.338
delta_Rv0954	-0.093	-0.678
PonA1	0.02	0.155
EccD1_KO	-0.566	-0.753
EspI_KO	-0.73	0.416
PE35_KO	-0.16	0.111
PPE68_KO	1.075	0.522
glycerol2	-0.559	-1.595
lignocerate	-0.296	-1.218
oleate	-0.345	-1.613
phosphatidylcholine	-0.071	-1.401
acetate	0.346	-0.229
glucAc	-0.08	0.392
Rv0950ko	0.766	0.154
Rv1096ko	0.856	0.76
Rv3684ko	-0.187	0.632
delta_otsA_trehalose	2.546	0.408