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 Rv0042c/-

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

	Rv1678/-	Rv0042c/-
Fe_supp_jason_reseq	-0.603	-0.429
low_pH_jason_reseq	2.096	2.832
NO_jason_reseq	-0.105	-1.168
B6_jason_reseq	-2.073	-1.443
MHCII_jason_reseq	0.526	0.527
Isoniazid02	-2.721	0.24
Rifampicin4	1.032	-0.915
Ethambutol3	-2.157	1.484
Meropenem3	-1.042	-0.53
Vancomycin16	-0.801	-1.47
Rv2680_day32	0.068	0.249
H37Rv_KO_MarP	-0.673	-1.381
hypoxia_3wks	-0.961	-2.703
hypoxia_6wks	0.497	-2.955
glycerol	1.333	0.231
cholesterol	0.264	-0.36
AJ	-0.585	-0.761
Bibs02	1.974	-0.319
Bibs02c	-0.399	-0.317
BL6	0.859	2.042
BL6a	1.69	0.644
BXD01	0.291	1.487
BXD010	0.912	1.227
BXD011	1.015	-0.026
BXD03	2.0	2.173
BXD04	1.013	1.113
BXD05	1.302	0.154
BXD06	0.543	0.511
BXD07	1.34	0.605
BXD08	0.878	0.793
BXD09	1.303	1.114
CAST	0.514	0.179
CCcont	1.385	2.186
DS01	1.465	-0.25
DS02	0.654	-0.54
DS04	1.546	-1.33
DS0c	-0.11	1.141
GP01	-0.077	1.385
GP02	-1.089	0.271
GP0c	0.573	2.192
NOD	0.264	-0.446
NZO	0.279	-0.04
PWK	-0.205	0.52
H37Rv_KO_CtpC	1.028	0.95
H37Rv_KO_CtpD	2.483	2.27
H37Rv_KO_Rv1272	0.501	1.846
H37Rv_KO_SugABC	-1.066	-1.157
H37Rv_KO_MbtN	2.197	1.155
Trans05	2.198	1.371
macrophage_unactivated	0.571	0.669
IL1	1.035	0.05
Rapamycin	0.436	-0.638
Tcell	-0.104	-0.176
GMCSF	0.451	-0.549
IFNab	1.206	-0.275
IFNg	-0.235	-1.539
IFNg_GMCSF1	-0.496	-0.984
Rv1432_day32	0.0	4.1
Rv1565c_day32	2.098	-0.415
secA2_input	-0.042	0.484
delta_Rv3594	0.858	2.183
delta_Rv3717	1.452	2.034
delta_Rv3811	1.17	1.828
delta_Rv0954	1.47	0.766
PonA1	1.133	0.856
EccD1_KO	0.164	-0.895
EspI_KO	0.787	-2.13
PE35_KO	0.618	-0.356
PPE68_KO	1.014	0.403
glycerol2	0.321	3.869
lignocerate	2.26	3.653
oleate	-1.983	-1.202
phosphatidylcholine	1.401	3.064
acetate	2.522	3.807
glucAc	2.538	3.201
Rv0950ko	-0.935	-0.476
Rv1096ko	-0.766	-2.063
Rv3684ko	0.223	-0.252
delta_otsA_trehalose	-1.065	0.739