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 Rv3268/-

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

	Rv1245c/-	Rv3268/-
Fe_supp_jason_reseq	-0.677	0.069
low_pH_jason_reseq	-0.534	-0.582
NO_jason_reseq	-0.084	-1.013
B6_jason_reseq	-1.086	-1.626
MHCII_jason_reseq	-0.021	-1.818
Isoniazid02	-0.386	-1.058
Rifampicin4	0.314	0.712
Ethambutol3	0.241	0.045
Meropenem3	0.183	-0.502
Vancomycin16	-0.082	0.016
Rv2680_day32	-0.198	-0.956
H37Rv_KO_MarP	-0.056	0.586
hypoxia_3wks	0.12	0.55
hypoxia_6wks	0.585	1.274
glycerol	-0.051	-0.543
cholesterol	-0.101	-0.704
AJ	-0.203	0.055
Bibs02	-0.886	0.278
Bibs02c	0.53	-0.918
BL6	-0.478	0.0
BL6a	0.352	-0.242
BXD01	-0.253	0.219
BXD010	-0.414	0.274
BXD011	-0.369	0.076
BXD03	-0.501	0.459
BXD04	0.764	0.568
BXD05	-0.012	0.288
BXD06	-0.081	0.785
BXD07	-0.401	-0.132
BXD08	1.002	0.16
BXD09	-0.36	0.395
CAST	-0.245	-0.329
CCcont	-0.305	-0.037
DS01	0.453	0.084
DS02	-0.211	-0.296
DS04	1.19	-0.134
DS0c	0.141	-0.135
GP01	0.677	1.864
GP02	1.268	1.292
GP0c	0.388	0.297
NOD	-0.303	-0.083
NZO	-0.533	-0.429
PWK	-0.421	-0.061
H37Rv_KO_CtpC	0.368	-0.122
H37Rv_KO_CtpD	0.321	-0.933
H37Rv_KO_Rv1272	0.179	0.076
H37Rv_KO_SugABC	0.017	-0.372
H37Rv_KO_MbtN	-0.179	0.21
Trans05	0.777	0.402
macrophage_unactivated	0.218	0.098
IL1	0.178	0.288
Rapamycin	0.184	0.939
Tcell	-0.453	0.365
GMCSF	0.235	0.726
IFNab	0.121	0.889
IFNg	0.08	0.337
IFNg_GMCSF1	0.707	0.657
Rv1432_day32	0.155	-0.271
Rv1565c_day32	-1.632	0.289
secA2_input	-0.798	0.429
delta_Rv3594	0.106	0.304
delta_Rv3717	0.273	0.481
delta_Rv3811	0.0	0.894
delta_Rv0954	-0.047	0.243
PonA1	0.285	0.451
EccD1_KO	0.668	0.168
EspI_KO	-0.068	-1.155
PE35_KO	0.306	0.128
PPE68_KO	-0.32	-0.739
glycerol2	0.06	0.276
lignocerate	-0.457	-0.018
oleate	0.411	0.359
phosphatidylcholine	-0.139	0.147
acetate	-0.426	-0.243
glucAc	-0.459	-0.327
Rv0950ko	0.063	0.163
Rv1096ko	0.0	0.368
Rv3684ko	0.233	0.537
delta_otsA_trehalose	-1.386	-1.794