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 Rv2659c/-:

update plot	correlation	link to info on gene
Rv3233c/-	(cc=0.5755)	info on Rv3233c/-
Rv1148c/-	(cc=0.5287)	info on Rv1148c/-
Rv2724c/fadE20	(cc=0.4854)	info on Rv2724c/fadE20
Rv2639c/-	(cc=0.4588)	info on Rv2639c/-
Rv1962c/vapC35	(cc=0.4575)	info on Rv1962c/vapC35
Rv3478/PPE60	(cc=0.4538)	info on Rv3478/PPE60
Rv3067/-	(cc=0.4331)	info on Rv3067/-
Rv3566c/nat	(cc=0.4296)	info on Rv3566c/nat
Rv2628/-	(cc=0.4188)	info on Rv2628/-
Rv2489c/-	(cc=0.4167)	info on Rv2489c/-

Correlation of Rv2659c/- with Rv2639c/-

Normalized LFCs for Rv2659c/-:
(description and provenance of datasets)

	Rv2659c/-	Rv2639c/-
Fe_supp_jason_reseq	0.035	0.068
low_pH_jason_reseq	-0.545	-0.085
NO_jason_reseq	-0.029	0.362
B6_jason_reseq	-0.051	0.114
MHCII_jason_reseq	0.522	0.077
Isoniazid02	-0.01	-2.072
Rifampicin4	-0.227	0.152
Ethambutol3	-0.091	-2.212
Meropenem3	-1.854	-2.692
Vancomycin16	-1.393	-1.276
Rv2680_day32	0.397	0.489
H37Rv_KO_MarP	0.277	0.965
hypoxia_3wks	-0.163	0.335
hypoxia_6wks	-0.163	0.426
glycerol	-0.268	-0.253
cholesterol	-0.358	-0.512
AJ	0.627	1.292
Bibs02	0.615	-0.623
Bibs02c	-0.023	-0.068
BL6	-0.11	-0.797
BL6a	0.022	-0.65
BXD01	-0.005	0.011
BXD010	-0.093	0.291
BXD011	0.129	-0.14
BXD03	0.005	-0.102
BXD04	0.088	0.692
BXD05	-0.265	0.194
BXD06	0.0	-0.031
BXD07	0.238	0.037
BXD08	0.366	0.041
BXD09	-0.186	-0.126
CAST	0.179	-0.242
CCcont	-0.454	-1.042
DS01	0.421	0.303
DS02	0.326	-0.071
DS04	0.37	-0.156
DS0c	0.393	-0.283
GP01	0.747	0.061
GP02	-0.669	1.528
GP0c	-0.12	0.714
NOD	1.3	-0.425
NZO	0.452	0.319
PWK	0.81	0.558
H37Rv_KO_CtpC	0.175	1.378
H37Rv_KO_CtpD	-0.41	-0.976
H37Rv_KO_Rv1272	0.529	0.208
H37Rv_KO_SugABC	0.774	0.621
H37Rv_KO_MbtN	-0.108	0.257
Trans05	-0.317	0.565
macrophage_unactivated	-0.325	-1.098
IL1	-0.359	-0.709
Rapamycin	-0.279	-0.282
Tcell	-0.072	-1.219
GMCSF	0.087	0.071
IFNab	-0.366	-0.484
IFNg	0.406	0.401
IFNg_GMCSF1	0.05	-0.88
Rv1432_day32	0.708	0.81
Rv1565c_day32	0.706	-1.278
secA2_input	0.146	0.283
delta_Rv3594	0.56	0.054
delta_Rv3717	0.028	0.299
delta_Rv3811	0.561	0.442
delta_Rv0954	0.267	0.196
PonA1	-0.364	0.807
EccD1_KO	0.408	1.667
EspI_KO	0.322	0.291
PE35_KO	0.265	0.729
PPE68_KO	0.499	1.334
glycerol2	-0.076	0.252
lignocerate	-0.211	-0.244
oleate	0.546	0.59
phosphatidylcholine	0.412	0.465
acetate	-0.687	-0.845
glucAc	-0.896	-1.314
Rv0950ko	0.081	0.084
Rv1096ko	0.211	-0.549
Rv3684ko	-0.183	-0.986
delta_otsA_trehalose	-0.7	-0.482