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 Rv1245c/-:

update plot	correlation	link to info on gene
Rv2088/pknJ	(cc=0.4545)	info on Rv2088/pknJ
Rv0731c/-	(cc=0.4479)	info on Rv0731c/-
Rv1831/-	(cc=0.4248)	info on Rv1831/-
Rv2770c/PPE44	(cc=0.4242)	info on Rv2770c/PPE44
Rv2695/-	(cc=0.418)	info on Rv2695/-
Rv0576/-	(cc=0.4057)	info on Rv0576/-
Rv2495c/bkdC	(cc=0.4046)	info on Rv2495c/bkdC
Rv3521/-	(cc=0.4045)	info on Rv3521/-
Rv2618/-	(cc=0.3913)	info on Rv2618/-
Rv3268/-	(cc=0.3895)	info on Rv3268/-

Correlation of Rv1245c/- with Rv0576/-

Normalized LFCs for Rv1245c/-:
(description and provenance of datasets)

	Rv1245c/-	Rv0576/-
Fe_supp_jason_reseq	-0.677	-0.308
low_pH_jason_reseq	-0.534	-0.475
NO_jason_reseq	-0.084	-0.205
B6_jason_reseq	-1.086	-1.345
MHCII_jason_reseq	-0.021	-0.823
Isoniazid02	-0.386	0.422
Rifampicin4	0.314	-0.292
Ethambutol3	0.241	0.311
Meropenem3	0.183	-0.374
Vancomycin16	-0.082	0.082
Rv2680_day32	-0.198	0.725
H37Rv_KO_MarP	-0.056	0.529
hypoxia_3wks	0.12	0.06
hypoxia_6wks	0.585	0.319
glycerol	-0.051	-1.257
cholesterol	-0.101	0.345
AJ	-0.203	-0.062
Bibs02	-0.886	0.494
Bibs02c	0.53	-0.611
BL6	-0.478	-0.841
BL6a	0.352	0.319
BXD01	-0.253	0.926
BXD010	-0.414	0.953
BXD011	-0.369	0.639
BXD03	-0.501	-0.279
BXD04	0.764	0.42
BXD05	-0.012	1.16
BXD06	-0.081	1.095
BXD07	-0.401	-0.037
BXD08	1.002	1.008
BXD09	-0.36	0.57
CAST	-0.245	-0.26
CCcont	-0.305	0.223
DS01	0.453	-0.267
DS02	-0.211	-0.878
DS04	1.19	1.067
DS0c	0.141	-0.379
GP01	0.677	0.511
GP02	1.268	2.078
GP0c	0.388	1.018
NOD	-0.303	0.06
NZO	-0.533	0.104
PWK	-0.421	-0.193
H37Rv_KO_CtpC	0.368	0.405
H37Rv_KO_CtpD	0.321	0.656
H37Rv_KO_Rv1272	0.179	0.585
H37Rv_KO_SugABC	0.017	-0.99
H37Rv_KO_MbtN	-0.179	0.013
Trans05	0.777	0.068
macrophage_unactivated	0.218	0.388
IL1	0.178	0.86
Rapamycin	0.184	1.2
Tcell	-0.453	1.03
GMCSF	0.235	-0.084
IFNab	0.121	0.327
IFNg	0.08	0.329
IFNg_GMCSF1	0.707	0.198
Rv1432_day32	0.155	0.721
Rv1565c_day32	-1.632	0.305
secA2_input	-0.798	-0.504
delta_Rv3594	0.106	0.919
delta_Rv3717	0.273	-0.263
delta_Rv3811	0.0	-0.81
delta_Rv0954	-0.047	0.102
PonA1	0.285	0.126
EccD1_KO	0.668	-0.444
EspI_KO	-0.068	-0.208
PE35_KO	0.306	0.283
PPE68_KO	-0.32	-0.234
glycerol2	0.06	-1.138
lignocerate	-0.457	-1.622
oleate	0.411	-0.322
phosphatidylcholine	-0.139	-0.958
acetate	-0.426	-1.012
glucAc	-0.459	-0.486
Rv0950ko	0.063	0.09
Rv1096ko	0.0	0.709
Rv3684ko	0.233	0.77
delta_otsA_trehalose	-1.386	-2.117