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 Rv0222/echA1:

update plot	correlation	link to info on gene
Rv3847/-	(cc=0.5955)	info on Rv3847/-
Rv3770B/-	(cc=0.5824)	info on Rv3770B/-
Rv2495c/bkdC	(cc=0.5804)	info on Rv2495c/bkdC
Rv3840/-	(cc=0.5591)	info on Rv3840/-
Rv0822c/-	(cc=0.5506)	info on Rv0822c/-
Rv0220/lipC	(cc=0.534)	info on Rv0220/lipC
Rv0971c/echA7	(cc=0.5292)	info on Rv0971c/echA7
Rv1787/PPE25	(cc=0.5288)	info on Rv1787/PPE25
Rv3146/nuoB	(cc=0.5256)	info on Rv3146/nuoB
Rv1551/plsB1	(cc=0.5196)	info on Rv1551/plsB1

Correlation of Rv0222/echA1 with Rv0971c/echA7

Normalized LFCs for Rv0222/echA1:
(description and provenance of datasets)

	Rv0222/echA1	Rv0971c/echA7
Fe_supp_jason_reseq	-3.435	-0.535
low_pH_jason_reseq	-2.431	-1.877
NO_jason_reseq	0.465	0.297
B6_jason_reseq	-3.258	-2.077
MHCII_jason_reseq	-1.782	-1.582
Isoniazid02	-0.8	0.243
Rifampicin4	-0.582	1.308
Ethambutol3	-0.164	1.133
Meropenem3	-0.258	0.879
Vancomycin16	-0.57	0.117
Rv2680_day32	-0.048	-0.022
H37Rv_KO_MarP	-0.138	0.378
hypoxia_3wks	0.63	-0.694
hypoxia_6wks	-0.065	-0.867
glycerol	-0.035	1.375
cholesterol	0.861	0.372
AJ	0.442	0.299
Bibs02	-0.237	0.29
Bibs02c	-0.887	-0.186
BL6	1.376	1.067
BL6a	0.672	1.085
BXD01	-0.046	0.483
BXD010	-0.191	1.122
BXD011	1.09	0.698
BXD03	1.092	1.026
BXD04	2.172	0.531
BXD05	1.202	1.583
BXD06	0.293	0.447
BXD07	0.891	1.171
BXD08	1.148	1.757
BXD09	0.863	1.271
CAST	0.662	0.561
CCcont	0.75	1.056
DS01	-0.306	0.34
DS02	0.625	0.934
DS04	2.54	2.478
DS0c	0.317	-0.591
GP01	1.765	0.185
GP02	1.928	1.92
GP0c	1.358	2.155
NOD	1.741	-0.875
NZO	-0.035	-0.932
PWK	-0.78	0.53
H37Rv_KO_CtpC	0.028	1.818
H37Rv_KO_CtpD	1.355	2.045
H37Rv_KO_Rv1272	-0.025	1.674
H37Rv_KO_SugABC	0.682	2.493
H37Rv_KO_MbtN	2.338	0.871
Trans05	-1.09	1.229
macrophage_unactivated	-0.035	0.641
IL1	1.207	0.982
Rapamycin	0.767	1.169
Tcell	0.342	-0.179
GMCSF	0.539	0.298
IFNab	-0.133	0.707
IFNg	0.059	0.166
IFNg_GMCSF1	0.101	0.71
Rv1432_day32	0.18	0.595
Rv1565c_day32	0.025	-0.847
secA2_input	-0.794	0.92
delta_Rv3594	-0.187	-0.902
delta_Rv3717	-0.607	-0.526
delta_Rv3811	-0.379	-0.815
delta_Rv0954	-0.242	-0.508
PonA1	-0.435	-1.144
EccD1_KO	-1.727	0.0
EspI_KO	-0.268	1.298
PE35_KO	0.175	-0.044
PPE68_KO	-0.909	-1.638
glycerol2	-0.888	0.116
lignocerate	-0.919	0.613
oleate	-0.207	-0.688
phosphatidylcholine	-0.689	0.332
acetate	-0.447	0.712
glucAc	-1.339	0.885
Rv0950ko	0.751	0.476
Rv1096ko	1.3	1.158
Rv3684ko	0.0	1.867
delta_otsA_trehalose	-0.267	0.768