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 Rv3234c/tgs3:

update plot	correlation	link to info on gene
Rv1425/-	(cc=0.4644)	info on Rv1425/-
Rv1249c/-	(cc=0.4583)	info on Rv1249c/-
Rv2405/-	(cc=0.449)	info on Rv2405/-
Rv0869c/moaA2	(cc=0.4471)	info on Rv0869c/moaA2
Rv3390/lpqD	(cc=0.4406)	info on Rv3390/lpqD
Rv1927/-	(cc=0.4393)	info on Rv1927/-
Rv0261c/narK3	(cc=0.4387)	info on Rv0261c/narK3
Rv3440c/-	(cc=0.4375)	info on Rv3440c/-
Rv0264c/-	(cc=0.4347)	info on Rv0264c/-
Rv2579/dhaA	(cc=0.4318)	info on Rv2579/dhaA

Correlation of Rv3234c/tgs3 with Rv2579/dhaA

Normalized LFCs for Rv3234c/tgs3:
(description and provenance of datasets)

	Rv3234c/tgs3	Rv2579/dhaA
Fe_supp_jason_reseq	-0.328	-0.407
low_pH_jason_reseq	-0.397	-0.845
NO_jason_reseq	-0.326	0.034
B6_jason_reseq	0.0	0.28
MHCII_jason_reseq	0.148	0.117
Isoniazid02	-0.314	0.655
Rifampicin4	0.403	0.498
Ethambutol3	0.531	0.878
Meropenem3	1.152	0.079
Vancomycin16	0.215	0.196
Rv2680_day32	0.77	0.432
H37Rv_KO_MarP	0.034	0.085
hypoxia_3wks	0.0	0.06
hypoxia_6wks	0.516	-0.077
glycerol	-0.255	-0.787
cholesterol	0.093	-0.824
AJ	0.166	0.657
Bibs02	-0.581	-0.411
Bibs02c	0.383	-0.138
BL6	-0.009	0.853
BL6a	0.356	-0.174
BXD01	-0.231	0.0
BXD010	0.009	-0.019
BXD011	-0.221	-0.104
BXD03	-0.216	0.152
BXD04	-0.085	-0.286
BXD05	-0.414	-0.515
BXD06	-0.081	-0.074
BXD07	-0.01	-0.135
BXD08	0.005	0.251
BXD09	0.244	-0.224
CAST	0.157	0.185
CCcont	-0.045	0.257
DS01	0.043	0.503
DS02	0.309	-0.31
DS04	-0.134	0.909
DS0c	-0.159	0.214
GP01	-0.856	0.084
GP02	1.097	1.387
GP0c	-0.148	-0.284
NOD	0.145	0.301
NZO	-0.21	0.551
PWK	0.092	0.925
H37Rv_KO_CtpC	0.111	-0.056
H37Rv_KO_CtpD	-0.899	-0.025
H37Rv_KO_Rv1272	0.669	0.441
H37Rv_KO_SugABC	0.014	0.436
H37Rv_KO_MbtN	0.16	0.208
Trans05	0.084	-0.073
macrophage_unactivated	0.366	0.685
IL1	0.543	0.534
Rapamycin	0.341	1.062
Tcell	0.235	0.587
GMCSF	-0.304	0.425
IFNab	0.336	0.311
IFNg	0.166	0.834
IFNg_GMCSF1	0.321	1.087
Rv1432_day32	0.494	0.36
Rv1565c_day32	0.171	0.169
secA2_input	0.146	-0.258
delta_Rv3594	-0.185	-0.038
delta_Rv3717	-0.074	0.128
delta_Rv3811	-0.443	-0.086
delta_Rv0954	0.067	0.245
PonA1	-0.594	-1.099
EccD1_KO	-0.74	0.309
EspI_KO	-0.351	0.222
PE35_KO	-0.152	0.732
PPE68_KO	-0.416	0.458
glycerol2	0.893	0.622
lignocerate	0.788	0.595
oleate	0.73	0.515
phosphatidylcholine	0.779	0.765
acetate	0.401	0.294
glucAc	0.4	0.055
Rv0950ko	0.808	0.021
Rv1096ko	0.28	0.241
Rv3684ko	0.37	-0.046
delta_otsA_trehalose	-0.768	-0.585