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 Rv1810/-

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

	Rv3547/ddn	Rv1810/-
Fe_supp_jason_reseq	-0.3	1.043
low_pH_jason_reseq	-0.744	-0.985
NO_jason_reseq	-0.129	-0.129
B6_jason_reseq	1.055	0.323
MHCII_jason_reseq	-0.104	-0.259
Isoniazid02	-0.613	0.687
Rifampicin4	0.309	-0.138
Ethambutol3	0.738	-0.134
Meropenem3	-0.062	-0.018
Vancomycin16	0.218	0.157
Rv2680_day32	-0.01	-0.329
H37Rv_KO_MarP	0.591	0.186
hypoxia_3wks	0.0	0.726
hypoxia_6wks	-0.044	1.113
glycerol	-0.459	0.08
cholesterol	-0.931	0.444
AJ	-0.113	-0.494
Bibs02	-0.117	0.305
Bibs02c	0.106	1.07
BL6	0.735	-0.06
BL6a	0.6	0.35
BXD01	0.497	0.237
BXD010	-0.082	0.392
BXD011	0.065	0.401
BXD03	-0.1	0.478
BXD04	0.734	0.056
BXD05	-0.191	0.303
BXD06	0.08	0.438
BXD07	0.547	0.238
BXD08	0.249	0.039
BXD09	0.386	0.571
CAST	0.269	-1.285
CCcont	0.376	0.166
DS01	-0.236	0.922
DS02	-0.205	0.298
DS04	0.063	0.922
DS0c	-0.456	0.182
GP01	-0.466	-0.053
GP02	0.162	1.283
GP0c	0.173	0.117
NOD	-0.177	-0.843
NZO	-0.826	-2.017
PWK	-0.705	-0.377
H37Rv_KO_CtpC	-0.179	0.433
H37Rv_KO_CtpD	-0.814	-0.54
H37Rv_KO_Rv1272	1.26	0.984
H37Rv_KO_SugABC	0.773	1.205
H37Rv_KO_MbtN	0.652	1.367
Trans05	0.638	1.513
macrophage_unactivated	0.619	0.126
IL1	-0.323	0.119
Rapamycin	0.068	-0.04
Tcell	0.766	0.613
GMCSF	-0.288	0.51
IFNab	-0.635	0.218
IFNg	-0.061	0.053
IFNg_GMCSF1	-0.17	-0.041
Rv1432_day32	-0.275	-0.169
Rv1565c_day32	0.324	-0.482
secA2_input	0.64	0.019
delta_Rv3594	0.415	1.091
delta_Rv3717	-0.083	0.491
delta_Rv3811	-0.336	0.486
delta_Rv0954	0.376	0.673
PonA1	0.893	0.45
EccD1_KO	0.27	0.691
EspI_KO	-0.573	-0.471
PE35_KO	-0.038	0.432
PPE68_KO	0.243	0.384
glycerol2	0.157	1.037
lignocerate	0.432	0.676
oleate	0.129	-0.323
phosphatidylcholine	0.345	1.036
acetate	-0.203	0.5
glucAc	0.012	-0.037
Rv0950ko	0.133	-0.745
Rv1096ko	0.35	-1.155
Rv3684ko	-0.92	-1.621
delta_otsA_trehalose	0.054	-0.243