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 Rv2808/-:

update plot	correlation	link to info on gene
Rv3697c/vapC48	(cc=0.5575)	info on Rv3697c/vapC48
Rv2647/-	(cc=0.5553)	info on Rv2647/-
Rv1205/-	(cc=0.5379)	info on Rv1205/-
Rv3018c/PPE46	(cc=0.5325)	info on Rv3018c/PPE46
Rv1260/-	(cc=0.5176)	info on Rv1260/-
Rv1646/PE17	(cc=0.5092)	info on Rv1646/PE17
Rv1206/fadD6	(cc=0.4987)	info on Rv1206/fadD6
Rv0755c/PPE12	(cc=0.4821)	info on Rv0755c/PPE12
Rv0554/bpoC	(cc=0.469)	info on Rv0554/bpoC
Rv2941/fadD28	(cc=0.4645)	info on Rv2941/fadD28

Correlation of Rv2808/- with Rv3018c/PPE46

Normalized LFCs for Rv2808/-:
(description and provenance of datasets)

	Rv2808/-	Rv3018c/PPE46
Fe_supp_jason_reseq	0.766	0.379
low_pH_jason_reseq	-0.124	-0.125
NO_jason_reseq	0.69	0.391
B6_jason_reseq	2.801	0.618
MHCII_jason_reseq	1.22	0.516
Isoniazid02	0.0	0.911
Rifampicin4	0.791	0.921
Ethambutol3	0.427	1.828
Meropenem3	0.444	0.552
Vancomycin16	0.775	0.446
Rv2680_day32	-3.002	0.505
H37Rv_KO_MarP	-0.114	0.274
hypoxia_3wks	-0.825	-0.471
hypoxia_6wks	0.023	-0.173
glycerol	-0.066	0.181
cholesterol	0.379	0.214
AJ	1.128	0.706
Bibs02	0.642	0.576
Bibs02c	-0.103	0.117
BL6	-0.255	0.246
BL6a	-0.502	0.304
BXD01	0.222	0.339
BXD010	0.472	0.369
BXD011	0.719	0.524
BXD03	0.266	0.274
BXD04	-0.061	-0.046
BXD05	-0.851	0.611
BXD06	0.246	0.556
BXD07	0.138	0.281
BXD08	0.66	0.433
BXD09	-0.314	0.208
CAST	1.565	0.676
CCcont	0.244	0.173
DS01	0.589	0.318
DS02	1.175	0.016
DS04	0.822	0.287
DS0c	0.848	0.107
GP01	-0.654	0.435
GP02	-0.764	0.288
GP0c	-0.577	-0.339
NOD	2.481	1.173
NZO	1.097	0.331
PWK	0.334	0.628
H37Rv_KO_CtpC	0.976	0.613
H37Rv_KO_CtpD	-1.163	0.758
H37Rv_KO_Rv1272	0.045	0.949
H37Rv_KO_SugABC	-0.929	0.64
H37Rv_KO_MbtN	0.264	0.582
Trans05	-1.679	0.563
macrophage_unactivated	-0.259	-0.117
IL1	-3.168	-0.807
Rapamycin	-0.948	-0.571
Tcell	-0.404	-1.062
GMCSF	-1.853	-0.536
IFNab	-1.808	-1.24
IFNg	-2.638	-1.018
IFNg_GMCSF1	-1.345	-0.613
Rv1432_day32	-1.675	0.229
Rv1565c_day32	-1.139	0.55
secA2_input	-0.504	-0.706
delta_Rv3594	-0.066	-0.128
delta_Rv3717	-1.057	-0.837
delta_Rv3811	-1.034	-0.333
delta_Rv0954	-1.495	-0.335
PonA1	-2.308	-0.404
EccD1_KO	-0.927	-0.22
EspI_KO	-0.091	0.163
PE35_KO	0.359	-0.02
PPE68_KO	-0.544	0.138
glycerol2	-0.433	0.807
lignocerate	0.145	1.119
oleate	-0.265	0.055
phosphatidylcholine	0.277	0.961
acetate	-0.382	0.987
glucAc	0.088	0.667
Rv0950ko	0.084	0.021
Rv1096ko	-0.262	-0.232
Rv3684ko	-0.481	-0.567
delta_otsA_trehalose	-2.072	-0.458