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 Rv2405/-

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

	Rv3234c/tgs3	Rv2405/-
Fe_supp_jason_reseq	-0.328	-0.863
low_pH_jason_reseq	-0.397	-0.249
NO_jason_reseq	-0.326	1.289
B6_jason_reseq	0.0	0.026
MHCII_jason_reseq	0.148	-0.023
Isoniazid02	-0.314	0.551
Rifampicin4	0.403	1.259
Ethambutol3	0.531	1.004
Meropenem3	1.152	1.991
Vancomycin16	0.215	0.915
Rv2680_day32	0.77	0.978
H37Rv_KO_MarP	0.034	0.549
hypoxia_3wks	0.0	-0.403
hypoxia_6wks	0.516	-0.633
glycerol	-0.255	-0.013
cholesterol	0.093	0.824
AJ	0.166	0.556
Bibs02	-0.581	-2.088
Bibs02c	0.383	-0.146
BL6	-0.009	0.346
BL6a	0.356	-0.636
BXD01	-0.231	-0.97
BXD010	0.009	-1.103
BXD011	-0.221	-0.769
BXD03	-0.216	-1.365
BXD04	-0.085	0.613
BXD05	-0.414	-0.845
BXD06	-0.081	-0.805
BXD07	-0.01	-1.193
BXD08	0.005	-0.972
BXD09	0.244	-1.346
CAST	0.157	0.439
CCcont	-0.045	-0.361
DS01	0.043	0.383
DS02	0.309	0.236
DS04	-0.134	-0.163
DS0c	-0.159	0.864
GP01	-0.856	0.541
GP02	1.097	0.673
GP0c	-0.148	1.023
NOD	0.145	-0.109
NZO	-0.21	-0.604
PWK	0.092	0.897
H37Rv_KO_CtpC	0.111	-0.923
H37Rv_KO_CtpD	-0.899	-0.052
H37Rv_KO_Rv1272	0.669	0.092
H37Rv_KO_SugABC	0.014	0.166
H37Rv_KO_MbtN	0.16	-0.66
Trans05	0.084	0.077
macrophage_unactivated	0.366	-0.543
IL1	0.543	-0.445
Rapamycin	0.341	-0.46
Tcell	0.235	-0.202
GMCSF	-0.304	-2.482
IFNab	0.336	-0.593
IFNg	0.166	-1.932
IFNg_GMCSF1	0.321	0.308
Rv1432_day32	0.494	1.116
Rv1565c_day32	0.171	1.369
secA2_input	0.146	0.607
delta_Rv3594	-0.185	0.584
delta_Rv3717	-0.074	-0.746
delta_Rv3811	-0.443	0.415
delta_Rv0954	0.067	0.986
PonA1	-0.594	1.944
EccD1_KO	-0.74	-0.793
EspI_KO	-0.351	0.533
PE35_KO	-0.152	-0.099
PPE68_KO	-0.416	-0.182
glycerol2	0.893	2.888
lignocerate	0.788	3.535
oleate	0.73	0.251
phosphatidylcholine	0.779	2.711
acetate	0.401	2.898
glucAc	0.4	2.694
Rv0950ko	0.808	1.049
Rv1096ko	0.28	1.662
Rv3684ko	0.37	1.064
delta_otsA_trehalose	-0.768	-1.856