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 Rv3440c/-

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

	Rv3234c/tgs3	Rv3440c/-
Fe_supp_jason_reseq	-0.328	-0.278
low_pH_jason_reseq	-0.397	-0.925
NO_jason_reseq	-0.326	-0.788
B6_jason_reseq	0.0	-0.178
MHCII_jason_reseq	0.148	-0.112
Isoniazid02	-0.314	0.838
Rifampicin4	0.403	0.85
Ethambutol3	0.531	0.817
Meropenem3	1.152	0.724
Vancomycin16	0.215	0.517
Rv2680_day32	0.77	0.505
H37Rv_KO_MarP	0.034	-0.023
hypoxia_3wks	0.0	0.152
hypoxia_6wks	0.516	0.0
glycerol	-0.255	0.758
cholesterol	0.093	0.088
AJ	0.166	0.615
Bibs02	-0.581	0.668
Bibs02c	0.383	0.299
BL6	-0.009	-0.197
BL6a	0.356	0.113
BXD01	-0.231	0.243
BXD010	0.009	-0.789
BXD011	-0.221	-1.159
BXD03	-0.216	-0.563
BXD04	-0.085	0.079
BXD05	-0.414	-0.97
BXD06	-0.081	-0.476
BXD07	-0.01	-0.377
BXD08	0.005	0.037
BXD09	0.244	0.019
CAST	0.157	0.417
CCcont	-0.045	-0.107
DS01	0.043	0.874
DS02	0.309	0.837
DS04	-0.134	0.86
DS0c	-0.159	0.701
GP01	-0.856	0.0
GP02	1.097	1.055
GP0c	-0.148	0.213
NOD	0.145	0.181
NZO	-0.21	0.811
PWK	0.092	0.244
H37Rv_KO_CtpC	0.111	0.537
H37Rv_KO_CtpD	-0.899	0.796
H37Rv_KO_Rv1272	0.669	0.343
H37Rv_KO_SugABC	0.014	1.312
H37Rv_KO_MbtN	0.16	0.29
Trans05	0.084	0.018
macrophage_unactivated	0.366	-0.464
IL1	0.543	-0.065
Rapamycin	0.341	0.178
Tcell	0.235	-0.42
GMCSF	-0.304	-0.293
IFNab	0.336	0.417
IFNg	0.166	0.222
IFNg_GMCSF1	0.321	0.101
Rv1432_day32	0.494	0.158
Rv1565c_day32	0.171	-0.316
secA2_input	0.146	-0.124
delta_Rv3594	-0.185	-0.285
delta_Rv3717	-0.074	-0.643
delta_Rv3811	-0.443	-0.223
delta_Rv0954	0.067	-0.398
PonA1	-0.594	-0.63
EccD1_KO	-0.74	-0.237
EspI_KO	-0.351	-0.011
PE35_KO	-0.152	-0.061
PPE68_KO	-0.416	-0.147
glycerol2	0.893	1.042
lignocerate	0.788	0.56
oleate	0.73	1.059
phosphatidylcholine	0.779	0.737
acetate	0.401	0.17
glucAc	0.4	-0.134
Rv0950ko	0.808	0.805
Rv1096ko	0.28	0.434
Rv3684ko	0.37	0.694
delta_otsA_trehalose	-0.768	-0.583