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 Rv1167c/-

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

	Rv3397c/phyA	Rv1167c/-
Fe_supp_jason_reseq	-0.665	-1.156
low_pH_jason_reseq	-0.343	0.448
NO_jason_reseq	0.512	1.88
B6_jason_reseq	-0.843	-2.005
MHCII_jason_reseq	-1.389	-2.389
Isoniazid02	-2.929	-2.878
Rifampicin4	-1.449	-1.338
Ethambutol3	-2.479	-1.589
Meropenem3	-1.773	-1.935
Vancomycin16	-1.273	-2.921
Rv2680_day32	-0.341	-1.565
H37Rv_KO_MarP	0.313	0.969
hypoxia_3wks	0.068	-0.159
hypoxia_6wks	0.591	-0.213
glycerol	0.856	0.088
cholesterol	0.676	-1.082
AJ	-0.8	-1.256
Bibs02	0.564	-1.06
Bibs02c	0.132	-0.708
BL6	2.198	0.775
BL6a	1.301	0.326
BXD01	1.656	0.869
BXD010	1.652	1.656
BXD011	1.667	0.865
BXD03	1.82	0.642
BXD04	1.101	0.882
BXD05	1.455	0.913
BXD06	1.683	0.495
BXD07	1.289	1.559
BXD08	1.938	1.349
BXD09	1.629	0.626
CAST	0.766	0.148
CCcont	2.127	1.736
DS01	0.729	-0.873
DS02	0.564	-1.26
DS04	-0.131	-0.228
DS0c	0.0	0.047
GP01	0.919	0.8
GP02	0.937	-0.835
GP0c	0.432	-0.089
NOD	0.903	-1.578
NZO	0.517	-0.614
PWK	0.124	-1.137
H37Rv_KO_CtpC	1.067	2.015
H37Rv_KO_CtpD	1.56	1.663
H37Rv_KO_Rv1272	0.744	0.455
H37Rv_KO_SugABC	1.18	-0.938
H37Rv_KO_MbtN	0.523	0.299
Trans05	0.082	0.443
macrophage_unactivated	0.369	0.249
IL1	0.742	0.866
Rapamycin	0.961	0.559
Tcell	0.427	1.636
GMCSF	0.417	0.481
IFNab	0.0	0.048
IFNg	0.901	0.673
IFNg_GMCSF1	0.233	0.751
Rv1432_day32	0.176	-1.949
Rv1565c_day32	0.861	-0.499
secA2_input	-1.363	0.266
delta_Rv3594	-0.052	0.693
delta_Rv3717	0.447	-0.021
delta_Rv3811	0.678	-0.617
delta_Rv0954	-0.044	-0.69
PonA1	0.076	0.0
EccD1_KO	0.743	0.661
EspI_KO	0.819	-0.722
PE35_KO	1.28	0.28
PPE68_KO	0.374	0.55
glycerol2	0.328	-0.319
lignocerate	0.677	-0.196
oleate	0.604	-0.906
phosphatidylcholine	0.71	0.032
acetate	0.181	0.17
glucAc	0.483	0.255
Rv0950ko	0.326	-1.357
Rv1096ko	0.582	-1.357
Rv3684ko	0.354	-1.153
delta_otsA_trehalose	0.481	-0.245