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 Rv2431c/PE25

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

	Rv0063/-	Rv2431c/PE25
Fe_supp_jason_reseq	-0.568	0.619
low_pH_jason_reseq	-0.172	0.522
NO_jason_reseq	-0.026	-0.914
B6_jason_reseq	0.872	-0.36
MHCII_jason_reseq	0.139	-0.217
Isoniazid02	-0.228	-0.931
Rifampicin4	0.0	-1.6
Ethambutol3	-0.134	-1.563
Meropenem3	0.037	-1.653
Vancomycin16	0.218	-0.921
Rv2680_day32	-0.874	-0.087
H37Rv_KO_MarP	0.775	-0.447
hypoxia_3wks	-0.805	0.582
hypoxia_6wks	-0.24	0.0
glycerol	1.176	3.461
cholesterol	2.914	6.0
AJ	0.788	1.303
Bibs02	-0.029	1.457
Bibs02c	0.587	1.199
BL6	0.621	1.457
BL6a	0.43	2.072
BXD01	-0.098	0.827
BXD010	0.261	0.551
BXD011	0.587	2.085
BXD03	0.756	1.534
BXD04	0.354	1.689
BXD05	0.599	2.296
BXD06	0.043	1.937
BXD07	0.148	2.139
BXD08	0.011	1.605
BXD09	-0.046	2.05
CAST	0.516	-0.192
CCcont	0.07	1.232
DS01	1.136	3.744
DS02	0.726	3.294
DS04	1.318	3.536
DS0c	0.662	2.665
GP01	0.201	0.531
GP02	-0.748	0.806
GP0c	-0.251	1.557
NOD	1.36	1.523
NZO	0.446	0.962
PWK	0.924	2.947
H37Rv_KO_CtpC	0.0	1.81
H37Rv_KO_CtpD	-0.283	1.079
H37Rv_KO_Rv1272	-0.233	2.011
H37Rv_KO_SugABC	0.942	1.484
H37Rv_KO_MbtN	0.276	0.09
Trans05	-0.548	2.411
macrophage_unactivated	-0.363	0.211
IL1	-0.053	0.561
Rapamycin	-0.835	0.233
Tcell	-0.606	0.72
GMCSF	0.166	-0.304
IFNab	0.0	0.668
IFNg	-0.048	0.786
IFNg_GMCSF1	-0.088	0.852
Rv1432_day32	-0.089	0.439
Rv1565c_day32	0.351	5.482
secA2_input	0.095	-1.575
delta_Rv3594	-0.159	0.425
delta_Rv3717	-0.458	0.174
delta_Rv3811	-0.607	0.013
delta_Rv0954	0.522	1.122
PonA1	0.658	0.196
EccD1_KO	-0.178	-0.72
EspI_KO	-0.317	-0.148
PE35_KO	0.271	0.639
PPE68_KO	0.266	0.64
glycerol2	0.048	-0.013
lignocerate	0.664	-0.468
oleate	-1.212	0.801
phosphatidylcholine	-0.253	0.162
acetate	0.484	-0.753
glucAc	0.575	-0.664
Rv0950ko	0.425	0.084
Rv1096ko	0.392	-1.197
Rv3684ko	0.747	-0.177
delta_otsA_trehalose	-0.535	0.513