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 Rv3815c/-

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

	Rv1817/-	Rv3815c/-
Fe_supp_jason_reseq	-0.223	0.979
low_pH_jason_reseq	-0.388	-0.796
NO_jason_reseq	-0.714	-0.126
B6_jason_reseq	-0.232	0.078
MHCII_jason_reseq	0.326	0.437
Isoniazid02	0.215	1.352
Rifampicin4	0.0	-0.631
Ethambutol3	0.612	1.757
Meropenem3	0.316	0.574
Vancomycin16	-0.04	-1.353
Rv2680_day32	-0.437	-2.585
H37Rv_KO_MarP	-0.186	0.539
hypoxia_3wks	0.116	-0.303
hypoxia_6wks	-0.203	-0.956
glycerol	0.604	0.942
cholesterol	0.241	0.987
AJ	-0.311	0.247
Bibs02	0.738	-0.274
Bibs02c	0.358	0.488
BL6	-0.327	0.605
BL6a	-0.133	0.432
BXD01	0.177	0.552
BXD010	-0.209	-0.555
BXD011	0.092	1.267
BXD03	-0.113	-0.091
BXD04	-0.103	0.913
BXD05	-0.219	-0.439
BXD06	0.007	-0.064
BXD07	-0.344	-0.093
BXD08	0.091	0.31
BXD09	-0.331	0.161
CAST	0.22	0.205
CCcont	-0.371	0.808
DS01	0.453	0.0
DS02	0.334	-1.134
DS04	0.332	0.364
DS0c	0.409	-0.471
GP01	-0.077	0.678
GP02	0.301	0.633
GP0c	-0.088	0.369
NOD	0.441	0.386
NZO	0.069	-0.257
PWK	0.068	0.413
H37Rv_KO_CtpC	0.111	-0.126
H37Rv_KO_CtpD	0.178	1.339
H37Rv_KO_Rv1272	1.0	1.376
H37Rv_KO_SugABC	-0.144	-0.298
H37Rv_KO_MbtN	0.43	0.907
Trans05	1.011	0.61
macrophage_unactivated	1.588	1.079
IL1	2.201	2.231
Rapamycin	2.317	2.397
Tcell	-4.923	-5.116
GMCSF	2.26	2.883
IFNab	1.886	2.352
IFNg	2.397	2.05
IFNg_GMCSF1	2.385	1.709
Rv1432_day32	0.096	0.15
Rv1565c_day32	-0.156	0.084
secA2_input	-0.434	-0.485
delta_Rv3594	0.0	0.327
delta_Rv3717	-0.028	1.309
delta_Rv3811	0.28	1.083
delta_Rv0954	0.142	0.976
PonA1	-0.059	0.616
EccD1_KO	0.687	0.918
EspI_KO	0.359	0.473
PE35_KO	0.63	-0.403
PPE68_KO	0.56	0.48
glycerol2	0.085	0.893
lignocerate	-0.069	0.992
oleate	0.386	0.379
phosphatidylcholine	0.239	0.769
acetate	-0.156	1.43
glucAc	-0.167	1.041
Rv0950ko	0.13	-0.498
Rv1096ko	-0.392	-0.115
Rv3684ko	-0.102	0.465
delta_otsA_trehalose	-0.085	-1.184