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 Rv2833c/ugpB:

update plot	correlation	link to info on gene
Rv2481c/-	(cc=0.6002)	info on Rv2481c/-
Rv2456c/-	(cc=0.5803)	info on Rv2456c/-
Rv2562/-	(cc=0.5305)	info on Rv2562/-
Rv0188/-	(cc=0.5302)	info on Rv0188/-
Rv0844c/narL	(cc=0.5279)	info on Rv0844c/narL
Rv0463/-	(cc=0.5193)	info on Rv0463/-
Rv1471/trxB1	(cc=0.5189)	info on Rv1471/trxB1
Rv0055/rpsR1	(cc=0.5066)	info on Rv0055/rpsR1
Rv1076/lipU	(cc=0.5061)	info on Rv1076/lipU
Rv0944/-	(cc=0.4935)	info on Rv0944/-

Correlation of Rv2833c/ugpB with Rv2456c/-

Normalized LFCs for Rv2833c/ugpB:
(description and provenance of datasets)

	Rv2833c/ugpB	Rv2456c/-
Fe_supp_jason_reseq	-1.047	-0.379
low_pH_jason_reseq	-0.855	-1.086
NO_jason_reseq	-0.496	0.0
B6_jason_reseq	-2.495	0.476
MHCII_jason_reseq	-1.705	-0.595
Isoniazid02	0.323	0.215
Rifampicin4	1.283	0.143
Ethambutol3	0.505	0.591
Meropenem3	0.497	-0.126
Vancomycin16	0.939	0.048
Rv2680_day32	1.035	0.302
H37Rv_KO_MarP	-0.188	0.071
hypoxia_3wks	0.0	-0.423
hypoxia_6wks	-0.234	0.355
glycerol	-0.693	-0.648
cholesterol	0.552	0.259
AJ	-0.541	-0.224
Bibs02	-0.736	-0.301
Bibs02c	-1.429	-0.076
BL6	1.972	0.922
BL6a	1.025	0.716
BXD01	0.8	0.662
BXD010	1.237	0.612
BXD011	0.812	1.502
BXD03	1.088	0.774
BXD04	0.67	1.111
BXD05	0.391	0.484
BXD06	0.91	0.863
BXD07	1.167	0.971
BXD08	1.509	0.717
BXD09	1.334	0.702
CAST	2.478	0.929
CCcont	1.651	0.332
DS01	-0.551	-0.399
DS02	0.699	0.0
DS04	-0.905	-0.128
DS0c	-0.506	0.061
GP01	-0.086	0.393
GP02	-0.568	0.291
GP0c	-0.237	0.461
NOD	0.0	0.428
NZO	0.309	0.321
PWK	-0.915	0.186
H37Rv_KO_CtpC	1.177	0.495
H37Rv_KO_CtpD	-1.086	-0.268
H37Rv_KO_Rv1272	1.385	0.562
H37Rv_KO_SugABC	-0.949	-0.214
H37Rv_KO_MbtN	-0.625	0.886
Trans05	1.851	1.071
macrophage_unactivated	0.65	-0.167
IL1	0.392	0.077
Rapamycin	0.921	-0.009
Tcell	0.903	0.502
GMCSF	0.731	0.185
IFNab	0.163	-0.212
IFNg	0.216	0.195
IFNg_GMCSF1	0.17	0.031
Rv1432_day32	-0.961	0.149
Rv1565c_day32	-0.24	-0.442
secA2_input	0.095	-0.092
delta_Rv3594	-0.402	0.138
delta_Rv3717	-0.802	0.457
delta_Rv3811	-0.651	-0.303
delta_Rv0954	-0.45	-0.521
PonA1	-0.799	-0.433
EccD1_KO	-1.47	0.556
EspI_KO	0.091	0.114
PE35_KO	0.443	-0.12
PPE68_KO	0.202	-0.266
glycerol2	0.873	0.338
lignocerate	1.376	0.813
oleate	0.489	0.386
phosphatidylcholine	1.108	0.829
acetate	1.079	0.068
glucAc	1.205	0.289
Rv0950ko	0.582	0.416
Rv1096ko	0.995	0.329
Rv3684ko	1.588	0.37
delta_otsA_trehalose	-1.327	-1.403