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 Rv3547/ddn:

update plot	correlation	link to info on gene
Rv1810/-	(cc=0.3693)	info on Rv1810/-
Rv1748/-	(cc=0.3647)	info on Rv1748/-
Rv2080/lppJ	(cc=0.3504)	info on Rv2080/lppJ
Rv1914c/-	(cc=0.3435)	info on Rv1914c/-
Rv3158/nuoN	(cc=0.337)	info on Rv3158/nuoN
Rv1472/echA12	(cc=0.3354)	info on Rv1472/echA12
Rv1951c/-	(cc=0.3263)	info on Rv1951c/-
Rv2456c/-	(cc=0.3259)	info on Rv2456c/-
Rv0755A/-	(cc=0.3256)	info on Rv0755A/-
Rv1885c/-	(cc=0.3226)	info on Rv1885c/-

Correlation of Rv3547/ddn with Rv2080/lppJ

Normalized LFCs for Rv3547/ddn:
(description and provenance of datasets)

	Rv3547/ddn	Rv2080/lppJ
Fe_supp_jason_reseq	-0.3	-0.421
low_pH_jason_reseq	-0.744	-0.174
NO_jason_reseq	-0.129	0.281
B6_jason_reseq	1.055	-0.121
MHCII_jason_reseq	-0.104	0.159
Isoniazid02	-0.613	0.189
Rifampicin4	0.309	0.138
Ethambutol3	0.738	1.274
Meropenem3	-0.062	-0.096
Vancomycin16	0.218	0.377
Rv2680_day32	-0.01	1.324
H37Rv_KO_MarP	0.591	-0.601
hypoxia_3wks	0.0	0.303
hypoxia_6wks	-0.044	-0.484
glycerol	-0.459	-0.9
cholesterol	-0.931	-1.074
AJ	-0.113	0.247
Bibs02	-0.117	0.397
Bibs02c	0.106	-0.975
BL6	0.735	0.733
BL6a	0.6	-0.096
BXD01	0.497	0.355
BXD010	-0.082	0.142
BXD011	0.065	0.453
BXD03	-0.1	1.171
BXD04	0.734	0.312
BXD05	-0.191	-0.505
BXD06	0.08	0.428
BXD07	0.547	0.296
BXD08	0.249	0.497
BXD09	0.386	0.533
CAST	0.269	0.969
CCcont	0.376	-0.156
DS01	-0.236	0.455
DS02	-0.205	0.019
DS04	0.063	0.162
DS0c	-0.456	-0.421
GP01	-0.466	1.498
GP02	0.162	0.362
GP0c	0.173	0.547
NOD	-0.177	0.543
NZO	-0.826	-0.983
PWK	-0.705	0.357
H37Rv_KO_CtpC	-0.179	0.186
H37Rv_KO_CtpD	-0.814	0.692
H37Rv_KO_Rv1272	1.26	1.607
H37Rv_KO_SugABC	0.773	1.653
H37Rv_KO_MbtN	0.652	0.224
Trans05	0.638	1.315
macrophage_unactivated	0.619	0.786
IL1	-0.323	0.0
Rapamycin	0.068	0.0
Tcell	0.766	-0.3
GMCSF	-0.288	-0.045
IFNab	-0.635	-0.26
IFNg	-0.061	-0.029
IFNg_GMCSF1	-0.17	0.465
Rv1432_day32	-0.275	0.077
Rv1565c_day32	0.324	-0.611
secA2_input	0.64	0.609
delta_Rv3594	0.415	0.411
delta_Rv3717	-0.083	0.07
delta_Rv3811	-0.336	-0.388
delta_Rv0954	0.376	-0.337
PonA1	0.893	0.801
EccD1_KO	0.27	0.02
EspI_KO	-0.573	0.619
PE35_KO	-0.038	-0.111
PPE68_KO	0.243	-0.208
glycerol2	0.157	-0.116
lignocerate	0.432	-0.437
oleate	0.129	-0.173
phosphatidylcholine	0.345	0.099
acetate	-0.203	-0.843
glucAc	0.012	-0.665
Rv0950ko	0.133	-0.118
Rv1096ko	0.35	-0.256
Rv3684ko	-0.92	-0.337
delta_otsA_trehalose	0.054	0.316