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 Rv3070/-:

update plot	correlation	link to info on gene
Rv1662/pks8	(cc=0.5061)	info on Rv1662/pks8
Rv1419/-	(cc=0.4987)	info on Rv1419/-
Rv0276/-	(cc=0.4657)	info on Rv0276/-
Rv2495c/bkdC	(cc=0.4624)	info on Rv2495c/bkdC
Rv0827c/kmtR	(cc=0.4484)	info on Rv0827c/kmtR
Rv3140/fadE23	(cc=0.4449)	info on Rv3140/fadE23
Rv2211c/gcvT	(cc=0.4339)	info on Rv2211c/gcvT
Rv3626c/-	(cc=0.4311)	info on Rv3626c/-
Rv2833c/ugpB	(cc=0.4288)	info on Rv2833c/ugpB
Rv2767c/-	(cc=0.4193)	info on Rv2767c/-

Correlation of Rv3070/- with Rv0276/-

Normalized LFCs for Rv3070/-:
(description and provenance of datasets)

	Rv3070/-	Rv0276/-
Fe_supp_jason_reseq	-0.529	-0.807
low_pH_jason_reseq	-0.878	-0.855
NO_jason_reseq	-0.494	-0.113
B6_jason_reseq	-1.15	0.322
MHCII_jason_reseq	-0.669	0.118
Isoniazid02	-0.035	0.141
Rifampicin4	-0.996	-0.23
Ethambutol3	-0.524	0.238
Meropenem3	-0.422	-0.272
Vancomycin16	-0.369	0.478
Rv2680_day32	0.899	0.73
H37Rv_KO_MarP	0.233	0.452
hypoxia_3wks	-0.088	-0.12
hypoxia_6wks	0.28	-0.194
glycerol	-0.788	-0.297
cholesterol	-0.981	0.193
AJ	1.077	0.277
Bibs02	0.838	0.335
Bibs02c	1.085	0.108
BL6	0.327	0.3
BL6a	1.378	0.112
BXD01	0.993	-0.035
BXD010	0.792	-0.135
BXD011	0.285	0.347
BXD03	1.018	-0.241
BXD04	0.43	0.613
BXD05	0.237	0.451
BXD06	1.196	-0.164
BXD07	0.75	0.421
BXD08	0.944	-0.287
BXD09	0.991	0.142
CAST	0.586	0.619
CCcont	1.06	-0.211
DS01	-0.068	0.525
DS02	0.469	0.714
DS04	1.018	0.177
DS0c	0.273	0.187
GP01	-0.706	0.094
GP02	-1.474	-1.435
GP0c	-0.117	-0.51
NOD	1.015	1.435
NZO	-0.724	-0.075
PWK	0.735	0.746
H37Rv_KO_CtpC	0.934	0.067
H37Rv_KO_CtpD	0.44	-0.282
H37Rv_KO_Rv1272	0.637	0.195
H37Rv_KO_SugABC	-1.705	-0.128
H37Rv_KO_MbtN	-1.164	-0.898
Trans05	0.445	0.061
macrophage_unactivated	0.726	0.139
IL1	0.771	0.706
Rapamycin	0.393	-0.258
Tcell	0.626	-0.098
GMCSF	0.317	-0.201
IFNab	0.212	0.112
IFNg	0.831	0.174
IFNg_GMCSF1	1.241	0.789
Rv1432_day32	-0.257	-0.1
Rv1565c_day32	0.12	-0.046
secA2_input	-0.177	0.928
delta_Rv3594	1.054	-0.441
delta_Rv3717	-1.258	-0.622
delta_Rv3811	0.043	-0.669
delta_Rv0954	0.89	0.557
PonA1	0.177	-0.44
EccD1_KO	-0.082	-0.26
EspI_KO	-0.736	-0.385
PE35_KO	1.138	-0.738
PPE68_KO	0.08	-0.618
glycerol2	0.342	0.135
lignocerate	0.485	0.418
oleate	0.116	0.262
phosphatidylcholine	0.312	0.28
acetate	0.146	-0.083
glucAc	0.102	0.051
Rv0950ko	0.709	1.604
Rv1096ko	1.173	1.514
Rv3684ko	2.227	1.837
delta_otsA_trehalose	0.049	1.079