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 Rv1667c/-:

update plot	correlation	link to info on gene
Rv2730/-	(cc=0.4737)	info on Rv2730/-
Rv2568c/-	(cc=0.4511)	info on Rv2568c/-
Rv2134c/-	(cc=0.4495)	info on Rv2134c/-
Rv1886c/fbpB	(cc=0.4388)	info on Rv1886c/fbpB
Rv1364c/-	(cc=0.4356)	info on Rv1364c/-
Rv2886c/-	(cc=0.4301)	info on Rv2886c/-
Rv3818/-	(cc=0.4265)	info on Rv3818/-
Rv3305c/amiA1	(cc=0.4225)	info on Rv3305c/amiA1
Rv0999/-	(cc=0.4204)	info on Rv0999/-
Rv3050c/-	(cc=0.4194)	info on Rv3050c/-

Correlation of Rv1667c/- with Rv3305c/amiA1

Normalized LFCs for Rv1667c/-:
(description and provenance of datasets)

	Rv1667c/-	Rv3305c/amiA1
Fe_supp_jason_reseq	0.344	-1.711
low_pH_jason_reseq	-0.241	-2.014
NO_jason_reseq	0.176	-0.454
B6_jason_reseq	-1.077	-1.483
MHCII_jason_reseq	0.53	0.372
Isoniazid02	0.473	-1.007
Rifampicin4	-0.658	0.062
Ethambutol3	-0.213	-0.337
Meropenem3	-0.404	-1.118
Vancomycin16	-0.464	-1.374
Rv2680_day32	1.135	0.595
H37Rv_KO_MarP	-0.538	-0.449
hypoxia_3wks	0.861	-1.252
hypoxia_6wks	0.491	0.814
glycerol	1.321	2.099
cholesterol	0.01	1.663
AJ	0.297	0.255
Bibs02	0.709	1.099
Bibs02c	0.182	-0.55
BL6	0.369	0.882
BL6a	0.479	0.0
BXD01	0.428	1.316
BXD010	0.363	-0.337
BXD011	0.54	0.226
BXD03	0.407	0.657
BXD04	0.863	1.303
BXD05	0.373	0.78
BXD06	0.651	0.941
BXD07	0.9	0.456
BXD08	1.084	1.626
BXD09	0.462	0.614
CAST	-0.239	0.172
CCcont	0.889	2.22
DS01	-0.091	0.778
DS02	0.578	-0.922
DS04	0.236	1.036
DS0c	0.096	0.313
GP01	1.166	0.527
GP02	0.274	-0.705
GP0c	0.689	0.231
NOD	0.584	0.324
NZO	0.131	-0.733
PWK	-0.091	-0.242
H37Rv_KO_CtpC	0.153	0.79
H37Rv_KO_CtpD	0.444	1.37
H37Rv_KO_Rv1272	1.011	1.885
H37Rv_KO_SugABC	-0.207	0.956
H37Rv_KO_MbtN	-0.178	0.747
Trans05	1.45	1.413
macrophage_unactivated	0.363	1.613
IL1	0.504	0.107
Rapamycin	0.792	0.988
Tcell	0.267	1.323
GMCSF	0.124	1.669
IFNab	1.046	-0.112
IFNg	0.032	-0.299
IFNg_GMCSF1	-0.116	0.0
Rv1432_day32	0.369	0.117
Rv1565c_day32	-0.03	1.039
secA2_input	0.158	-1.781
delta_Rv3594	0.233	1.173
delta_Rv3717	1.169	0.593
delta_Rv3811	0.404	0.561
delta_Rv0954	1.001	-0.067
PonA1	0.671	0.085
EccD1_KO	0.405	-0.477
EspI_KO	0.898	-0.174
PE35_KO	0.583	-0.554
PPE68_KO	0.47	-1.84
glycerol2	-0.036	0.252
lignocerate	0.296	-0.387
oleate	-1.136	-1.229
phosphatidylcholine	-0.31	-1.535
acetate	0.475	-1.006
glucAc	0.221	-1.159
Rv0950ko	0.292	-1.155
Rv1096ko	-0.021	-0.148
Rv3684ko	-0.655	-1.153
delta_otsA_trehalose	-0.103	1.247