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 Rv1903/-

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

	Rv1678/-	Rv1903/-
Fe_supp_jason_reseq	-0.603	-0.494
low_pH_jason_reseq	2.096	0.201
NO_jason_reseq	-0.105	0.326
B6_jason_reseq	-2.073	0.009
MHCII_jason_reseq	0.526	-0.026
Isoniazid02	-2.721	-0.428
Rifampicin4	1.032	0.715
Ethambutol3	-2.157	0.736
Meropenem3	-1.042	0.062
Vancomycin16	-0.801	-0.377
Rv2680_day32	0.068	-0.724
H37Rv_KO_MarP	-0.673	0.007
hypoxia_3wks	-0.961	0.108
hypoxia_6wks	0.497	0.42
glycerol	1.333	0.853
cholesterol	0.264	0.798
AJ	-0.585	0.272
Bibs02	1.974	0.685
Bibs02c	-0.399	0.72
BL6	0.859	0.643
BL6a	1.69	0.994
BXD01	0.291	0.498
BXD010	0.912	0.819
BXD011	1.015	0.688
BXD03	2.0	0.833
BXD04	1.013	0.019
BXD05	1.302	1.199
BXD06	0.543	0.051
BXD07	1.34	0.645
BXD08	0.878	0.246
BXD09	1.303	1.085
CAST	0.514	1.151
CCcont	1.385	0.138
DS01	1.465	-0.334
DS02	0.654	-0.087
DS04	1.546	-0.446
DS0c	-0.11	0.478
GP01	-0.077	0.354
GP02	-1.089	-0.653
GP0c	0.573	0.286
NOD	0.264	0.026
NZO	0.279	-0.692
PWK	-0.205	0.456
H37Rv_KO_CtpC	1.028	1.599
H37Rv_KO_CtpD	2.483	2.544
H37Rv_KO_Rv1272	0.501	1.104
H37Rv_KO_SugABC	-1.066	-2.204
H37Rv_KO_MbtN	2.197	0.75
Trans05	2.198	1.641
macrophage_unactivated	0.571	-0.679
IL1	1.035	0.872
Rapamycin	0.436	0.457
Tcell	-0.104	0.531
GMCSF	0.451	1.249
IFNab	1.206	-0.227
IFNg	-0.235	0.668
IFNg_GMCSF1	-0.496	-0.339
Rv1432_day32	0.0	0.87
Rv1565c_day32	2.098	0.504
secA2_input	-0.042	-1.28
delta_Rv3594	0.858	0.069
delta_Rv3717	1.452	-0.255
delta_Rv3811	1.17	0.529
delta_Rv0954	1.47	0.121
PonA1	1.133	0.092
EccD1_KO	0.164	0.579
EspI_KO	0.787	0.707
PE35_KO	0.618	-0.131
PPE68_KO	1.014	0.659
glycerol2	0.321	0.448
lignocerate	2.26	0.756
oleate	-1.983	0.069
phosphatidylcholine	1.401	0.448
acetate	2.522	0.687
glucAc	2.538	0.922
Rv0950ko	-0.935	0.214
Rv1096ko	-0.766	-1.227
Rv3684ko	0.223	-0.026
delta_otsA_trehalose	-1.065	-0.832