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 Rv0063/-:

update plot	correlation	link to info on gene
Rv1675c/cmr	(cc=0.5603)	info on Rv1675c/cmr
Rv0669c/-	(cc=0.5197)	info on Rv0669c/-
Rv0338c/-	(cc=0.5024)	info on Rv0338c/-
Rv3283/sseA	(cc=0.4817)	info on Rv3283/sseA
Rv2268c/cyp128	(cc=0.4799)	info on Rv2268c/cyp128
Rv1371/-	(cc=0.4686)	info on Rv1371/-
Rv2431c/PE25	(cc=0.4568)	info on Rv2431c/PE25
Rv3509c/ilvX	(cc=0.4437)	info on Rv3509c/ilvX
Rv3154/nuoJ	(cc=0.4374)	info on Rv3154/nuoJ
Rv3529c/-	(cc=0.435)	info on Rv3529c/-

Correlation of Rv0063/- with Rv3154/nuoJ

Normalized LFCs for Rv0063/-:
(description and provenance of datasets)

	Rv0063/-	Rv3154/nuoJ
Fe_supp_jason_reseq	-0.568	-0.246
low_pH_jason_reseq	-0.172	-0.785
NO_jason_reseq	-0.026	-0.41
B6_jason_reseq	0.872	1.378
MHCII_jason_reseq	0.139	-1.236
Isoniazid02	-0.228	-0.068
Rifampicin4	0.0	1.356
Ethambutol3	-0.134	0.276
Meropenem3	0.037	1.718
Vancomycin16	0.218	0.738
Rv2680_day32	-0.874	-0.504
H37Rv_KO_MarP	0.775	-0.991
hypoxia_3wks	-0.805	0.49
hypoxia_6wks	-0.24	1.002
glycerol	1.176	1.916
cholesterol	2.914	6.0
AJ	0.788	0.632
Bibs02	-0.029	1.76
Bibs02c	0.587	0.556
BL6	0.621	0.576
BL6a	0.43	-0.395
BXD01	-0.098	0.643
BXD010	0.261	0.195
BXD011	0.587	0.74
BXD03	0.756	-0.639
BXD04	0.354	0.89
BXD05	0.599	0.101
BXD06	0.043	0.644
BXD07	0.148	0.493
BXD08	0.011	0.663
BXD09	-0.046	0.392
CAST	0.516	0.549
CCcont	0.07	-0.079
DS01	1.136	2.587
DS02	0.726	2.28
DS04	1.318	0.936
DS0c	0.662	3.386
GP01	0.201	-0.724
GP02	-0.748	-0.984
GP0c	-0.251	0.236
NOD	1.36	0.812
NZO	0.446	-0.355
PWK	0.924	-0.797
H37Rv_KO_CtpC	0.0	0.284
H37Rv_KO_CtpD	-0.283	1.421
H37Rv_KO_Rv1272	-0.233	0.819
H37Rv_KO_SugABC	0.942	0.768
H37Rv_KO_MbtN	0.276	-0.889
Trans05	-0.548	1.263
macrophage_unactivated	-0.363	-0.928
IL1	-0.053	-1.038
Rapamycin	-0.835	-1.117
Tcell	-0.606	-0.3
GMCSF	0.166	-0.671
IFNab	0.0	0.354
IFNg	-0.048	-1.376
IFNg_GMCSF1	-0.088	1.719
Rv1432_day32	-0.089	0.407
Rv1565c_day32	0.351	0.251
secA2_input	0.095	-0.717
delta_Rv3594	-0.159	-0.698
delta_Rv3717	-0.458	0.074
delta_Rv3811	-0.607	-0.364
delta_Rv0954	0.522	-0.411
PonA1	0.658	-0.07
EccD1_KO	-0.178	0.296
EspI_KO	-0.317	-0.53
PE35_KO	0.271	0.035
PPE68_KO	0.266	0.691
glycerol2	0.048	1.426
lignocerate	0.664	-0.972
oleate	-1.212	1.469
phosphatidylcholine	-0.253	-0.721
acetate	0.484	-0.535
glucAc	0.575	0.746
Rv0950ko	0.425	1.067
Rv1096ko	0.392	0.748
Rv3684ko	0.747	0.377
delta_otsA_trehalose	-0.535	1.672