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 Rv2778c/-:

update plot	correlation	link to info on gene
Rv2275/-	(cc=0.5281)	info on Rv2275/-
Rv0844c/narL	(cc=0.5199)	info on Rv0844c/narL
Rv0260c/-	(cc=0.5162)	info on Rv0260c/-
Rv2809/-	(cc=0.5132)	info on Rv2809/-
Rv2481c/-	(cc=0.4888)	info on Rv2481c/-
Rv1583c/-	(cc=0.4835)	info on Rv1583c/-
Rv1504c/-	(cc=0.479)	info on Rv1504c/-
Rv1167c/-	(cc=0.4756)	info on Rv1167c/-
Rv1548c/PPE21	(cc=0.4716)	info on Rv1548c/PPE21
Rv2818c/-	(cc=0.466)	info on Rv2818c/-

Correlation of Rv2778c/- with Rv2275/-

Normalized LFCs for Rv2778c/-:
(description and provenance of datasets)

	Rv2778c/-	Rv2275/-
Fe_supp_jason_reseq	0.668	0.827
low_pH_jason_reseq	0.517	0.617
NO_jason_reseq	-0.087	-0.244
B6_jason_reseq	-0.436	-0.7
MHCII_jason_reseq	-0.471	0.61
Isoniazid02	-0.291	0.153
Rifampicin4	-0.046	0.975
Ethambutol3	-0.251	0.188
Meropenem3	-0.732	0.352
Vancomycin16	-0.854	0.539
Rv2680_day32	-2.125	-0.471
H37Rv_KO_MarP	0.062	0.08
hypoxia_3wks	0.267	0.128
hypoxia_6wks	0.079	-0.288
glycerol	0.569	-0.453
cholesterol	-0.068	0.184
AJ	0.413	0.294
Bibs02	-0.971	1.13
Bibs02c	-1.384	-0.47
BL6	0.865	0.864
BL6a	0.306	0.528
BXD01	0.507	1.203
BXD010	0.37	0.816
BXD011	0.447	1.745
BXD03	-0.051	1.025
BXD04	0.374	0.0
BXD05	1.071	0.615
BXD06	1.063	0.39
BXD07	0.951	0.602
BXD08	1.473	0.871
BXD09	0.809	1.087
CAST	-0.367	-1.054
CCcont	0.794	1.179
DS01	0.106	0.503
DS02	0.266	0.142
DS04	-0.752	0.929
DS0c	-1.185	-0.231
GP01	0.563	-0.354
GP02	-0.072	-0.523
GP0c	-0.651	-0.986
NOD	-2.11	-0.239
NZO	-0.056	1.306
PWK	-0.608	-1.232
H37Rv_KO_CtpC	1.184	1.545
H37Rv_KO_CtpD	0.134	1.255
H37Rv_KO_Rv1272	1.414	2.719
H37Rv_KO_SugABC	-1.521	2.705
H37Rv_KO_MbtN	2.179	1.924
Trans05	0.036	1.729
macrophage_unactivated	0.483	1.215
IL1	-1.121	-0.089
Rapamycin	-0.973	1.114
Tcell	-0.254	0.873
GMCSF	0.768	0.51
IFNab	-0.115	0.088
IFNg	1.077	0.516
IFNg_GMCSF1	-0.606	-1.656
Rv1432_day32	-0.043	-0.411
Rv1565c_day32	-0.665	0.3
secA2_input	-2.037	-1.681
delta_Rv3594	-0.343	-0.725
delta_Rv3717	-1.024	-0.927
delta_Rv3811	-1.063	-0.796
delta_Rv0954	-1.128	-1.708
PonA1	-0.689	-0.936
EccD1_KO	0.22	2.111
EspI_KO	0.066	1.443
PE35_KO	0.811	1.17
PPE68_KO	0.579	1.872
glycerol2	0.479	0.0
lignocerate	0.491	0.505
oleate	0.109	0.0
phosphatidylcholine	0.543	0.415
acetate	0.449	1.014
glucAc	0.337	0.487
Rv0950ko	-0.983	-1.354
Rv1096ko	-1.336	-0.835
Rv3684ko	-1.418	-1.179
delta_otsA_trehalose	-0.367	-0.836