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 Rv3390/lpqD

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

	Rv3234c/tgs3	Rv3390/lpqD
Fe_supp_jason_reseq	-0.328	-0.23
low_pH_jason_reseq	-0.397	-1.22
NO_jason_reseq	-0.326	-0.341
B6_jason_reseq	0.0	-0.213
MHCII_jason_reseq	0.148	-0.257
Isoniazid02	-0.314	0.457
Rifampicin4	0.403	0.011
Ethambutol3	0.531	0.074
Meropenem3	1.152	0.654
Vancomycin16	0.215	0.119
Rv2680_day32	0.77	1.066
H37Rv_KO_MarP	0.034	0.395
hypoxia_3wks	0.0	-0.347
hypoxia_6wks	0.516	-0.411
glycerol	-0.255	-0.407
cholesterol	0.093	-0.02
AJ	0.166	0.136
Bibs02	-0.581	0.322
Bibs02c	0.383	-0.003
BL6	-0.009	-0.755
BL6a	0.356	-0.119
BXD01	-0.231	-0.646
BXD010	0.009	-0.19
BXD011	-0.221	0.013
BXD03	-0.216	0.074
BXD04	-0.085	-0.068
BXD05	-0.414	-0.457
BXD06	-0.081	-0.201
BXD07	-0.01	-0.313
BXD08	0.005	-0.228
BXD09	0.244	-0.187
CAST	0.157	0.08
CCcont	-0.045	-0.316
DS01	0.043	0.181
DS02	0.309	-0.34
DS04	-0.134	-0.134
DS0c	-0.159	0.148
GP01	-0.856	0.032
GP02	1.097	0.696
GP0c	-0.148	-0.519
NOD	0.145	-0.495
NZO	-0.21	-0.142
PWK	0.092	0.463
H37Rv_KO_CtpC	0.111	0.162
H37Rv_KO_CtpD	-0.899	0.737
H37Rv_KO_Rv1272	0.669	0.784
H37Rv_KO_SugABC	0.014	-0.314
H37Rv_KO_MbtN	0.16	-0.112
Trans05	0.084	0.391
macrophage_unactivated	0.366	0.331
IL1	0.543	-0.208
Rapamycin	0.341	0.046
Tcell	0.235	-0.114
GMCSF	-0.304	1.061
IFNab	0.336	0.139
IFNg	0.166	0.059
IFNg_GMCSF1	0.321	0.578
Rv1432_day32	0.494	0.567
Rv1565c_day32	0.171	-0.16
secA2_input	0.146	-0.056
delta_Rv3594	-0.185	0.017
delta_Rv3717	-0.074	-0.396
delta_Rv3811	-0.443	-0.367
delta_Rv0954	0.067	0.081
PonA1	-0.594	-0.601
EccD1_KO	-0.74	-0.349
EspI_KO	-0.351	-0.55
PE35_KO	-0.152	-0.309
PPE68_KO	-0.416	-0.678
glycerol2	0.893	0.706
lignocerate	0.788	0.605
oleate	0.73	0.447
phosphatidylcholine	0.779	0.451
acetate	0.401	0.229
glucAc	0.4	0.118
Rv0950ko	0.808	0.724
Rv1096ko	0.28	0.148
Rv3684ko	0.37	-0.151
delta_otsA_trehalose	-0.768	0.45