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 Rv1817/-:

update plot	correlation	link to info on gene
Rv2113/-	(cc=0.8479)	info on Rv2113/-
Rv0453/PPE11	(cc=0.8091)	info on Rv0453/PPE11
Rv2848c/cobB	(cc=0.7965)	info on Rv2848c/cobB
Rv2822c/-	(cc=0.7829)	info on Rv2822c/-
Rv0159c/PE3	(cc=0.7688)	info on Rv0159c/PE3
Rv3815c/-	(cc=0.7673)	info on Rv3815c/-
Rv3862c/whiB6	(cc=0.5436)	info on Rv3862c/whiB6
Rv2339/mmpL9	(cc=0.5212)	info on Rv2339/mmpL9
Rv3685c/cyp137	(cc=0.5029)	info on Rv3685c/cyp137
Rv2389c/rpfD	(cc=0.5017)	info on Rv2389c/rpfD

Correlation of Rv1817/- with Rv3862c/whiB6

Normalized LFCs for Rv1817/-:
(description and provenance of datasets)

	Rv1817/-	Rv3862c/whiB6
Fe_supp_jason_reseq	-0.223	0.27
low_pH_jason_reseq	-0.388	-0.684
NO_jason_reseq	-0.714	-1.972
B6_jason_reseq	-0.232	-0.517
MHCII_jason_reseq	0.326	-0.251
Isoniazid02	0.215	0.413
Rifampicin4	0.0	-0.449
Ethambutol3	0.612	-0.202
Meropenem3	0.316	-0.734
Vancomycin16	-0.04	0.475
Rv2680_day32	-0.437	1.898
H37Rv_KO_MarP	-0.186	0.056
hypoxia_3wks	0.116	-0.016
hypoxia_6wks	-0.203	0.192
glycerol	0.604	1.258
cholesterol	0.241	0.721
AJ	-0.311	-0.664
Bibs02	0.738	0.543
Bibs02c	0.358	0.599
BL6	-0.327	0.536
BL6a	-0.133	0.479
BXD01	0.177	0.764
BXD010	-0.209	0.886
BXD011	0.092	0.576
BXD03	-0.113	-0.231
BXD04	-0.103	0.935
BXD05	-0.219	1.023
BXD06	0.007	0.67
BXD07	-0.344	0.533
BXD08	0.091	0.625
BXD09	-0.331	0.533
CAST	0.22	-0.452
CCcont	-0.371	0.604
DS01	0.453	0.814
DS02	0.334	-0.882
DS04	0.332	0.247
DS0c	0.409	-0.228
GP01	-0.077	-0.202
GP02	0.301	-0.347
GP0c	-0.088	0.624
NOD	0.441	0.384
NZO	0.069	0.152
PWK	0.068	-0.176
H37Rv_KO_CtpC	0.111	0.534
H37Rv_KO_CtpD	0.178	1.006
H37Rv_KO_Rv1272	1.0	1.051
H37Rv_KO_SugABC	-0.144	0.796
H37Rv_KO_MbtN	0.43	1.909
Trans05	1.011	1.106
macrophage_unactivated	1.588	0.931
IL1	2.201	2.005
Rapamycin	2.317	1.234
Tcell	-4.923	-1.623
GMCSF	2.26	0.837
IFNab	1.886	3.586
IFNg	2.397	2.705
IFNg_GMCSF1	2.385	2.124
Rv1432_day32	0.096	0.257
Rv1565c_day32	-0.156	-0.655
secA2_input	-0.434	-0.675
delta_Rv3594	0.0	0.491
delta_Rv3717	-0.028	1.436
delta_Rv3811	0.28	0.803
delta_Rv0954	0.142	-1.081
PonA1	-0.059	-0.926
EccD1_KO	0.687	-0.391
EspI_KO	0.359	-0.836
PE35_KO	0.63	-0.753
PPE68_KO	0.56	-0.611
glycerol2	0.085	0.395
lignocerate	-0.069	-0.448
oleate	0.386	0.937
phosphatidylcholine	0.239	0.071
acetate	-0.156	-0.941
glucAc	-0.167	-1.946
Rv0950ko	0.13	-1.366
Rv1096ko	-0.392	-0.995
Rv3684ko	-0.102	-0.373
delta_otsA_trehalose	-0.085	-1.32