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 Rv3527/-:

update plot	correlation	link to info on gene
Rv0822c/-	(cc=0.5028)	info on Rv0822c/-
Rv1931c/-	(cc=0.496)	info on Rv1931c/-
Rv0805/-	(cc=0.4792)	info on Rv0805/-
Rv3126c/-	(cc=0.4772)	info on Rv3126c/-
Rv2211c/gcvT	(cc=0.4745)	info on Rv2211c/gcvT
Rv2389c/rpfD	(cc=0.4624)	info on Rv2389c/rpfD
Rv0388c/PPE9	(cc=0.449)	info on Rv0388c/PPE9
Rv2543/lppA	(cc=0.448)	info on Rv2543/lppA
Rv0371c/-	(cc=0.4478)	info on Rv0371c/-
Rv3398c/idsA1	(cc=0.4451)	info on Rv3398c/idsA1

Correlation of Rv3527/- with Rv2389c/rpfD

Normalized LFCs for Rv3527/-:
(description and provenance of datasets)

	Rv3527/-	Rv2389c/rpfD
Fe_supp_jason_reseq	-0.24	-0.362
low_pH_jason_reseq	-1.989	-0.435
NO_jason_reseq	-1.352	0.197
B6_jason_reseq	-2.055	-0.716
MHCII_jason_reseq	-1.933	-0.625
Isoniazid02	-0.239	0.086
Rifampicin4	0.812	0.049
Ethambutol3	0.275	-0.016
Meropenem3	0.423	2.093
Vancomycin16	0.745	-0.064
Rv2680_day32	1.206	0.647
H37Rv_KO_MarP	-0.693	0.553
hypoxia_3wks	-0.494	0.355
hypoxia_6wks	-0.319	-0.019
glycerol	0.505	0.891
cholesterol	-1.583	-0.168
AJ	0.249	0.0
Bibs02	-0.909	-0.17
Bibs02c	1.805	0.435
BL6	-0.231	0.489
BL6a	2.069	0.672
BXD01	-0.455	-0.141
BXD010	0.306	0.577
BXD011	1.804	0.542
BXD03	1.376	0.242
BXD04	0.796	0.34
BXD05	0.306	0.563
BXD06	0.377	0.173
BXD07	1.06	0.135
BXD08	0.551	-0.097
BXD09	1.178	0.337
CAST	0.277	0.135
CCcont	-0.109	-0.29
DS01	0.033	0.026
DS02	-0.032	-0.047
DS04	1.525	0.342
DS0c	0.204	-0.286
GP01	-1.967	0.004
GP02	-1.658	0.234
GP0c	-2.081	0.43
NOD	0.866	0.298
NZO	0.883	-0.176
PWK	-0.465	0.128
H37Rv_KO_CtpC	0.97	0.735
H37Rv_KO_CtpD	0.303	0.486
H37Rv_KO_Rv1272	-0.285	1.233
H37Rv_KO_SugABC	-1.355	0.781
H37Rv_KO_MbtN	-1.41	0.418
Trans05	-0.841	0.521
macrophage_unactivated	-0.054	0.597
IL1	-0.178	0.887
Rapamycin	0.859	1.148
Tcell	0.081	-0.994
GMCSF	-0.203	0.969
IFNab	0.886	0.865
IFNg	0.131	1.264
IFNg_GMCSF1	0.518	1.458
Rv1432_day32	-0.356	0.332
Rv1565c_day32	-1.579	0.482
secA2_input	-1.293	-0.178
delta_Rv3594	-2.424	-0.202
delta_Rv3717	-0.856	-0.321
delta_Rv3811	-3.15	-0.586
delta_Rv0954	-2.507	-0.295
PonA1	-1.009	0.614
EccD1_KO	-0.299	0.812
EspI_KO	1.691	0.633
PE35_KO	0.181	0.534
PPE68_KO	-0.042	0.195
glycerol2	-1.871	-0.581
lignocerate	-1.626	-1.078
oleate	-1.095	0.302
phosphatidylcholine	-2.451	-0.294
acetate	-1.006	-1.282
glucAc	-1.764	-1.315
Rv0950ko	0.82	0.443
Rv1096ko	-0.124	0.169
Rv3684ko	0.586	0.144
delta_otsA_trehalose	0.722	1.314