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 Rv3039c/echA17:

update plot	correlation	link to info on gene
Rv0781/ptrBa	(cc=0.4406)	info on Rv0781/ptrBa
Rv0427c/xthA	(cc=0.4258)	info on Rv0427c/xthA
Rv0948c/-	(cc=0.423)	info on Rv0948c/-
Rv1114/vapC32	(cc=0.4088)	info on Rv1114/vapC32
Rv2767c/-	(cc=0.4001)	info on Rv2767c/-
Rv2290/lppO	(cc=0.3994)	info on Rv2290/lppO
Rv1869c/-	(cc=0.3929)	info on Rv1869c/-
Rv1233c/-	(cc=0.3912)	info on Rv1233c/-
Rv0553/menC	(cc=0.3836)	info on Rv0553/menC
Rv3189/-	(cc=0.3816)	info on Rv3189/-

Correlation of Rv3039c/echA17 with Rv3189/-

Normalized LFCs for Rv3039c/echA17:
(description and provenance of datasets)

	Rv3039c/echA17	Rv3189/-
Fe_supp_jason_reseq	-0.923	0.772
low_pH_jason_reseq	-2.652	-0.999
NO_jason_reseq	0.457	-0.478
B6_jason_reseq	0.461	0.781
MHCII_jason_reseq	1.475	0.581
Isoniazid02	0.767	-0.464
Rifampicin4	-1.202	0.054
Ethambutol3	0.0	-0.096
Meropenem3	0.146	0.024
Vancomycin16	-0.231	-0.027
Rv2680_day32	2.205	-0.389
H37Rv_KO_MarP	0.363	0.047
hypoxia_3wks	-0.128	0.044
hypoxia_6wks	0.37	-0.023
glycerol	-1.24	-0.503
cholesterol	0.233	-0.052
AJ	0.938	0.227
Bibs02	-1.325	0.468
Bibs02c	1.69	0.067
BL6	0.321	0.155
BL6a	2.177	0.056
BXD01	0.242	-0.562
BXD010	1.779	0.212
BXD011	1.263	-0.076
BXD03	0.0	-0.958
BXD04	0.199	0.14
BXD05	1.773	0.084
BXD06	0.824	0.279
BXD07	1.209	0.176
BXD08	0.71	-0.505
BXD09	1.425	-0.027
CAST	0.254	0.606
CCcont	0.797	-0.084
DS01	1.42	0.406
DS02	-0.572	1.09
DS04	-1.093	0.173
DS0c	0.605	0.33
GP01	-1.322	-0.436
GP02	-1.114	0.244
GP0c	-1.19	-1.256
NOD	-0.508	0.511
NZO	0.767	0.184
PWK	-0.918	0.05
H37Rv_KO_CtpC	-1.729	-0.125
H37Rv_KO_CtpD	-1.348	0.511
H37Rv_KO_Rv1272	-1.747	-0.028
H37Rv_KO_SugABC	-0.978	-2.002
H37Rv_KO_MbtN	-0.747	-0.939
Trans05	-1.619	0.477
macrophage_unactivated	-0.133	0.013
IL1	0.356	0.679
Rapamycin	1.126	0.657
Tcell	-0.818	-0.632
GMCSF	0.705	0.314
IFNab	0.305	0.583
IFNg	0.665	0.345
IFNg_GMCSF1	0.129	0.663
Rv1432_day32	0.0	0.733
Rv1565c_day32	1.151	0.256
secA2_input	1.368	0.111
delta_Rv3594	1.127	0.941
delta_Rv3717	0.707	0.159
delta_Rv3811	1.903	0.358
delta_Rv0954	0.398	0.388
PonA1	-0.56	1.267
EccD1_KO	1.23	1.592
EspI_KO	1.914	1.494
PE35_KO	0.58	1.205
PPE68_KO	1.814	1.142
glycerol2	-0.761	-0.914
lignocerate	-0.874	-0.609
oleate	-0.89	-0.882
phosphatidylcholine	-1.14	-0.902
acetate	-1.807	-0.763
glucAc	-0.949	-0.317
Rv0950ko	-0.112	-0.018
Rv1096ko	0.323	-0.217
Rv3684ko	0.35	-1.022
delta_otsA_trehalose	0.322	0.337