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 Rv1678/-:

update plot	correlation	link to info on gene
Rv0940c/-	(cc=0.5598)	info on Rv0940c/-
Rv2738c/-	(cc=0.5484)	info on Rv2738c/-
Rv2544/lppB	(cc=0.4987)	info on Rv2544/lppB
Rv2558/-	(cc=0.472)	info on Rv2558/-
Rv3473c/bpoA	(cc=0.4718)	info on Rv3473c/bpoA
Rv1167c/-	(cc=0.4715)	info on Rv1167c/-
Rv1903/-	(cc=0.4691)	info on Rv1903/-
Rv3045/adhC	(cc=0.468)	info on Rv3045/adhC
Rv3397c/phyA	(cc=0.4679)	info on Rv3397c/phyA
Rv0042c/-	(cc=0.465)	info on Rv0042c/-

Correlation of Rv1678/- with Rv0940c/-

Normalized LFCs for Rv1678/-:
(description and provenance of datasets)

	Rv1678/-	Rv0940c/-
Fe_supp_jason_reseq	-0.603	-0.546
low_pH_jason_reseq	2.096	-0.445
NO_jason_reseq	-0.105	0.126
B6_jason_reseq	-2.073	-0.989
MHCII_jason_reseq	0.526	-0.421
Isoniazid02	-2.721	-4.434
Rifampicin4	1.032	0.482
Ethambutol3	-2.157	-3.779
Meropenem3	-1.042	-4.315
Vancomycin16	-0.801	-1.417
Rv2680_day32	0.068	0.113
H37Rv_KO_MarP	-0.673	-0.255
hypoxia_3wks	-0.961	-0.841
hypoxia_6wks	0.497	0.754
glycerol	1.333	0.316
cholesterol	0.264	0.168
AJ	-0.585	0.57
Bibs02	1.974	-1.015
Bibs02c	-0.399	-0.311
BL6	0.859	0.847
BL6a	1.69	0.284
BXD01	0.291	0.715
BXD010	0.912	1.34
BXD011	1.015	0.711
BXD03	2.0	0.332
BXD04	1.013	1.328
BXD05	1.302	0.263
BXD06	0.543	1.327
BXD07	1.34	1.065
BXD08	0.878	0.743
BXD09	1.303	0.917
CAST	0.514	0.754
CCcont	1.385	1.0
DS01	1.465	0.719
DS02	0.654	0.736
DS04	1.546	1.234
DS0c	-0.11	-0.102
GP01	-0.077	0.312
GP02	-1.089	-0.803
GP0c	0.573	-0.446
NOD	0.264	0.469
NZO	0.279	1.52
PWK	-0.205	0.254
H37Rv_KO_CtpC	1.028	0.585
H37Rv_KO_CtpD	2.483	0.147
H37Rv_KO_Rv1272	0.501	1.095
H37Rv_KO_SugABC	-1.066	0.088
H37Rv_KO_MbtN	2.197	0.528
Trans05	2.198	0.895
macrophage_unactivated	0.571	-0.082
IL1	1.035	-0.317
Rapamycin	0.436	-0.16
Tcell	-0.104	0.205
GMCSF	0.451	-0.137
IFNab	1.206	-1.868
IFNg	-0.235	-1.446
IFNg_GMCSF1	-0.496	-1.197
Rv1432_day32	0.0	1.249
Rv1565c_day32	2.098	0.692
secA2_input	-0.042	-0.863
delta_Rv3594	0.858	-0.571
delta_Rv3717	1.452	-0.691
delta_Rv3811	1.17	-0.663
delta_Rv0954	1.47	-1.222
PonA1	1.133	-1.092
EccD1_KO	0.164	0.089
EspI_KO	0.787	1.087
PE35_KO	0.618	0.522
PPE68_KO	1.014	0.65
glycerol2	0.321	1.375
lignocerate	2.26	2.046
oleate	-1.983	-0.469
phosphatidylcholine	1.401	1.426
acetate	2.522	1.812
glucAc	2.538	1.613
Rv0950ko	-0.935	-0.482
Rv1096ko	-0.766	-0.115
Rv3684ko	0.223	-0.524
delta_otsA_trehalose	-1.065	0.254