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 Rv3397c/phyA

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

	Rv1678/-	Rv3397c/phyA
Fe_supp_jason_reseq	-0.603	-0.665
low_pH_jason_reseq	2.096	-0.343
NO_jason_reseq	-0.105	0.512
B6_jason_reseq	-2.073	-0.843
MHCII_jason_reseq	0.526	-1.389
Isoniazid02	-2.721	-2.929
Rifampicin4	1.032	-1.449
Ethambutol3	-2.157	-2.479
Meropenem3	-1.042	-1.773
Vancomycin16	-0.801	-1.273
Rv2680_day32	0.068	-0.341
H37Rv_KO_MarP	-0.673	0.313
hypoxia_3wks	-0.961	0.068
hypoxia_6wks	0.497	0.591
glycerol	1.333	0.856
cholesterol	0.264	0.676
AJ	-0.585	-0.8
Bibs02	1.974	0.564
Bibs02c	-0.399	0.132
BL6	0.859	2.198
BL6a	1.69	1.301
BXD01	0.291	1.656
BXD010	0.912	1.652
BXD011	1.015	1.667
BXD03	2.0	1.82
BXD04	1.013	1.101
BXD05	1.302	1.455
BXD06	0.543	1.683
BXD07	1.34	1.289
BXD08	0.878	1.938
BXD09	1.303	1.629
CAST	0.514	0.766
CCcont	1.385	2.127
DS01	1.465	0.729
DS02	0.654	0.564
DS04	1.546	-0.131
DS0c	-0.11	0.0
GP01	-0.077	0.919
GP02	-1.089	0.937
GP0c	0.573	0.432
NOD	0.264	0.903
NZO	0.279	0.517
PWK	-0.205	0.124
H37Rv_KO_CtpC	1.028	1.067
H37Rv_KO_CtpD	2.483	1.56
H37Rv_KO_Rv1272	0.501	0.744
H37Rv_KO_SugABC	-1.066	1.18
H37Rv_KO_MbtN	2.197	0.523
Trans05	2.198	0.082
macrophage_unactivated	0.571	0.369
IL1	1.035	0.742
Rapamycin	0.436	0.961
Tcell	-0.104	0.427
GMCSF	0.451	0.417
IFNab	1.206	0.0
IFNg	-0.235	0.901
IFNg_GMCSF1	-0.496	0.233
Rv1432_day32	0.0	0.176
Rv1565c_day32	2.098	0.861
secA2_input	-0.042	-1.363
delta_Rv3594	0.858	-0.052
delta_Rv3717	1.452	0.447
delta_Rv3811	1.17	0.678
delta_Rv0954	1.47	-0.044
PonA1	1.133	0.076
EccD1_KO	0.164	0.743
EspI_KO	0.787	0.819
PE35_KO	0.618	1.28
PPE68_KO	1.014	0.374
glycerol2	0.321	0.328
lignocerate	2.26	0.677
oleate	-1.983	0.604
phosphatidylcholine	1.401	0.71
acetate	2.522	0.181
glucAc	2.538	0.483
Rv0950ko	-0.935	0.326
Rv1096ko	-0.766	0.582
Rv3684ko	0.223	0.354
delta_otsA_trehalose	-1.065	0.481