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 Rv0831c/-

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

	Rv3397c/phyA	Rv0831c/-
Fe_supp_jason_reseq	-0.665	-0.095
low_pH_jason_reseq	-0.343	-0.795
NO_jason_reseq	0.512	-0.181
B6_jason_reseq	-0.843	-0.576
MHCII_jason_reseq	-1.389	-0.507
Isoniazid02	-2.929	-2.738
Rifampicin4	-1.449	-0.284
Ethambutol3	-2.479	-0.525
Meropenem3	-1.773	-0.074
Vancomycin16	-1.273	-0.141
Rv2680_day32	-0.341	-0.171
H37Rv_KO_MarP	0.313	0.205
hypoxia_3wks	0.068	0.447
hypoxia_6wks	0.591	0.875
glycerol	0.856	-1.346
cholesterol	0.676	0.227
AJ	-0.8	-0.094
Bibs02	0.564	0.817
Bibs02c	0.132	-0.474
BL6	2.198	0.909
BL6a	1.301	0.676
BXD01	1.656	0.486
BXD010	1.652	0.649
BXD011	1.667	1.237
BXD03	1.82	1.058
BXD04	1.101	1.061
BXD05	1.455	0.354
BXD06	1.683	0.441
BXD07	1.289	0.482
BXD08	1.938	0.487
BXD09	1.629	0.943
CAST	0.766	0.991
CCcont	2.127	0.444
DS01	0.729	0.44
DS02	0.564	0.67
DS04	-0.131	0.378
DS0c	0.0	0.105
GP01	0.919	0.0
GP02	0.937	1.084
GP0c	0.432	0.516
NOD	0.903	1.429
NZO	0.517	0.429
PWK	0.124	0.703
H37Rv_KO_CtpC	1.067	0.401
H37Rv_KO_CtpD	1.56	0.638
H37Rv_KO_Rv1272	0.744	1.234
H37Rv_KO_SugABC	1.18	1.089
H37Rv_KO_MbtN	0.523	0.23
Trans05	0.082	1.402
macrophage_unactivated	0.369	-0.297
IL1	0.742	-0.193
Rapamycin	0.961	-0.779
Tcell	0.427	-0.046
GMCSF	0.417	-0.048
IFNab	0.0	-0.405
IFNg	0.901	-0.037
IFNg_GMCSF1	0.233	-0.192
Rv1432_day32	0.176	0.206
Rv1565c_day32	0.861	-0.161
secA2_input	-1.363	-0.014
delta_Rv3594	-0.052	-0.121
delta_Rv3717	0.447	-0.578
delta_Rv3811	0.678	0.23
delta_Rv0954	-0.044	0.11
PonA1	0.076	0.179
EccD1_KO	0.743	0.441
EspI_KO	0.819	0.813
PE35_KO	1.28	-0.414
PPE68_KO	0.374	-0.214
glycerol2	0.328	0.629
lignocerate	0.677	0.727
oleate	0.604	0.432
phosphatidylcholine	0.71	0.162
acetate	0.181	0.05
glucAc	0.483	0.037
Rv0950ko	0.326	0.19
Rv1096ko	0.582	0.166
Rv3684ko	0.354	0.219
delta_otsA_trehalose	0.481	0.456