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 Rv3397c/phyA:

update plot	correlation	link to info on gene
Rv1167c/-	(cc=0.6612)	info on Rv1167c/-
Rv0940c/-	(cc=0.6497)	info on Rv0940c/-
Rv3153/nuoI	(cc=0.6383)	info on Rv3153/nuoI
Rv0231/fadE4	(cc=0.6367)	info on Rv0231/fadE4
Rv0260c/-	(cc=0.6193)	info on Rv0260c/-
Rv2390c/-	(cc=0.608)	info on Rv2390c/-
Rv3300c/-	(cc=0.6029)	info on Rv3300c/-
Rv1500/-	(cc=0.6019)	info on Rv1500/-
Rv1430/PE16	(cc=0.6003)	info on Rv1430/PE16
Rv0831c/-	(cc=0.5876)	info on Rv0831c/-

Correlation of Rv3397c/phyA with Rv3153/nuoI

Normalized LFCs for Rv3397c/phyA:
(description and provenance of datasets)

	Rv3397c/phyA	Rv3153/nuoI
Fe_supp_jason_reseq	-0.665	-0.287
low_pH_jason_reseq	-0.343	0.087
NO_jason_reseq	0.512	-0.641
B6_jason_reseq	-0.843	-0.048
MHCII_jason_reseq	-1.389	-1.143
Isoniazid02	-2.929	-0.831
Rifampicin4	-1.449	0.171
Ethambutol3	-2.479	-0.833
Meropenem3	-1.773	-1.41
Vancomycin16	-1.273	-1.037
Rv2680_day32	-0.341	0.447
H37Rv_KO_MarP	0.313	-0.653
hypoxia_3wks	0.068	1.089
hypoxia_6wks	0.591	0.8
glycerol	0.856	0.233
cholesterol	0.676	-0.306
AJ	-0.8	-0.168
Bibs02	0.564	-0.466
Bibs02c	0.132	0.274
BL6	2.198	1.6
BL6a	1.301	1.855
BXD01	1.656	1.737
BXD010	1.652	1.805
BXD011	1.667	2.199
BXD03	1.82	1.505
BXD04	1.101	1.562
BXD05	1.455	1.926
BXD06	1.683	1.917
BXD07	1.289	1.59
BXD08	1.938	2.086
BXD09	1.629	1.922
CAST	0.766	0.04
CCcont	2.127	1.069
DS01	0.729	0.616
DS02	0.564	0.896
DS04	-0.131	0.426
DS0c	0.0	1.771
GP01	0.919	0.68
GP02	0.937	0.875
GP0c	0.432	0.823
NOD	0.903	-0.291
NZO	0.517	0.0
PWK	0.124	-0.293
H37Rv_KO_CtpC	1.067	0.611
H37Rv_KO_CtpD	1.56	1.755
H37Rv_KO_Rv1272	0.744	1.526
H37Rv_KO_SugABC	1.18	0.935
H37Rv_KO_MbtN	0.523	0.018
Trans05	0.082	1.287
macrophage_unactivated	0.369	-0.199
IL1	0.742	-0.469
Rapamycin	0.961	-0.11
Tcell	0.427	-0.029
GMCSF	0.417	0.52
IFNab	0.0	0.571
IFNg	0.901	-0.294
IFNg_GMCSF1	0.233	-0.085
Rv1432_day32	0.176	0.259
Rv1565c_day32	0.861	-0.218
secA2_input	-1.363	-0.379
delta_Rv3594	-0.052	-0.647
delta_Rv3717	0.447	-0.211
delta_Rv3811	0.678	0.0
delta_Rv0954	-0.044	-0.526
PonA1	0.076	-0.396
EccD1_KO	0.743	0.467
EspI_KO	0.819	0.0
PE35_KO	1.28	0.592
PPE68_KO	0.374	0.682
glycerol2	0.328	1.883
lignocerate	0.677	-0.582
oleate	0.604	2.298
phosphatidylcholine	0.71	-0.669
acetate	0.181	-0.259
glucAc	0.483	0.54
Rv0950ko	0.326	0.136
Rv1096ko	0.582	0.054
Rv3684ko	0.354	-0.18
delta_otsA_trehalose	0.481	-0.029