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 Rv1290A/-:

update plot	correlation	link to info on gene
Rv1725c/-	(cc=0.5786)	info on Rv1725c/-
Rv2613c/-	(cc=0.5346)	info on Rv2613c/-
Rv0089/-	(cc=0.5223)	info on Rv0089/-
Rv3167c/-	(cc=0.522)	info on Rv3167c/-
Rv2019/-	(cc=0.5198)	info on Rv2019/-
Rv2517c/-	(cc=0.5142)	info on Rv2517c/-
Rv0396/-	(cc=0.5124)	info on Rv0396/-
Rv2405/-	(cc=0.5115)	info on Rv2405/-
Rv3056/dinP	(cc=0.5052)	info on Rv3056/dinP
Rv1999c/-	(cc=0.5003)	info on Rv1999c/-

Correlation of Rv1290A/- with Rv0089/-

Normalized LFCs for Rv1290A/-:
(description and provenance of datasets)

	Rv1290A/-	Rv0089/-
Fe_supp_jason_reseq	1.441	-0.617
low_pH_jason_reseq	-1.282	-0.221
NO_jason_reseq	0.11	0.047
B6_jason_reseq	-0.771	0.241
MHCII_jason_reseq	0.935	0.487
Isoniazid02	-0.685	0.877
Rifampicin4	-0.13	-0.701
Ethambutol3	-0.349	-0.483
Meropenem3	1.52	-0.564
Vancomycin16	-0.194	0.0
Rv2680_day32	-0.359	1.554
H37Rv_KO_MarP	0.025	1.943
hypoxia_3wks	-0.339	-0.59
hypoxia_6wks	-1.539	-0.699
glycerol	-1.624	-1.188
cholesterol	-0.218	-0.61
AJ	-0.602	0.069
Bibs02	-0.223	0.098
Bibs02c	-0.796	0.0
BL6	-0.1	-1.724
BL6a	-1.538	-1.411
BXD01	-1.563	-1.681
BXD010	-0.559	-1.478
BXD011	-1.384	-1.727
BXD03	-0.617	-1.397
BXD04	-1.76	-0.973
BXD05	-2.96	-1.529
BXD06	-1.187	-1.642
BXD07	-1.505	-2.006
BXD08	-2.361	-2.382
BXD09	-1.382	-1.596
CAST	-0.06	0.492
CCcont	-0.937	-0.977
DS01	-1.032	-0.209
DS02	-0.993	0.153
DS04	0.119	0.462
DS0c	-1.215	0.308
GP01	-0.574	0.326
GP02	2.507	-1.336
GP0c	-0.337	-0.489
NOD	-0.371	0.145
NZO	-1.835	-0.1
PWK	0.365	0.389
H37Rv_KO_CtpC	0.743	-1.138
H37Rv_KO_CtpD	-2.438	-3.064
H37Rv_KO_Rv1272	-1.022	-0.742
H37Rv_KO_SugABC	1.676	-0.481
H37Rv_KO_MbtN	1.666	-1.571
Trans05	0.298	0.008
macrophage_unactivated	-1.259	-2.727
IL1	0.552	-1.246
Rapamycin	0.436	-2.071
Tcell	-0.166	-1.3
GMCSF	-1.415	-1.848
IFNab	-2.331	-2.524
IFNg	-0.422	-1.871
IFNg_GMCSF1	-0.496	-0.936
Rv1432_day32	0.0	0.301
Rv1565c_day32	0.556	0.594
secA2_input	-1.67	-1.028
delta_Rv3594	0.092	0.0
delta_Rv3717	-0.96	-0.216
delta_Rv3811	-0.29	0.755
delta_Rv0954	-0.596	0.442
PonA1	-0.439	-0.308
EccD1_KO	-0.086	-0.118
EspI_KO	1.791	1.221
PE35_KO	2.345	0.204
PPE68_KO	1.955	1.497
glycerol2	1.401	1.494
lignocerate	1.386	1.736
oleate	0.0	-0.505
phosphatidylcholine	1.594	1.304
acetate	2.79	2.168
glucAc	1.825	1.508
Rv0950ko	1.251	-0.169
Rv1096ko	1.028	0.983
Rv3684ko	2.021	1.019
delta_otsA_trehalose	-1.964	1.304