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 Rv1366/-:

update plot	correlation	link to info on gene
Rv3749c/-	(cc=0.6056)	info on Rv3749c/-
Rv2078/-	(cc=0.5622)	info on Rv2078/-
Rv1913/-	(cc=0.5434)	info on Rv1913/-
Rv1013/pks16	(cc=0.5409)	info on Rv1013/pks16
Rv2287/yjcE	(cc=0.5232)	info on Rv2287/yjcE
Rv1751/-	(cc=0.5193)	info on Rv1751/-
Rv3697c/vapC48	(cc=0.5103)	info on Rv3697c/vapC48
Rv3819/-	(cc=0.4989)	info on Rv3819/-
Rv0226c/-	(cc=0.4983)	info on Rv0226c/-
Rv0235c/-	(cc=0.4943)	info on Rv0235c/-

Correlation of Rv1366/- with Rv2078/-

Normalized LFCs for Rv1366/-:
(description and provenance of datasets)

	Rv1366/-	Rv2078/-
Fe_supp_jason_reseq	-0.884	-1.478
low_pH_jason_reseq	-0.172	1.154
NO_jason_reseq	-0.294	-3.715
B6_jason_reseq	-0.871	-1.004
MHCII_jason_reseq	-0.267	-1.831
Isoniazid02	0.148	0.648
Rifampicin4	-0.376	0.211
Ethambutol3	0.269	-0.505
Meropenem3	0.237	-0.701
Vancomycin16	0.172	0.499
Rv2680_day32	-0.969	0.0
H37Rv_KO_MarP	0.518	1.411
hypoxia_3wks	-0.235	-1.655
hypoxia_6wks	-0.048	2.629
glycerol	-0.78	-2.499
cholesterol	-0.44	-2.008
AJ	0.134	-0.316
Bibs02	-0.823	1.325
Bibs02c	0.656	-0.674
BL6	0.376	0.307
BL6a	0.397	0.042
BXD01	0.834	2.42
BXD010	1.115	0.379
BXD011	0.35	1.575
BXD03	-0.278	0.189
BXD04	0.315	-0.472
BXD05	0.231	-0.151
BXD06	0.323	2.187
BXD07	0.476	0.673
BXD08	0.506	0.782
BXD09	-0.012	1.71
CAST	-0.142	0.752
CCcont	0.646	1.474
DS01	0.301	0.286
DS02	-0.254	-0.296
DS04	0.263	0.89
DS0c	0.525	0.343
GP01	1.227	-1.64
GP02	1.296	-1.382
GP0c	0.54	-2.16
NOD	0.148	1.347
NZO	0.839	-0.043
PWK	0.406	1.712
H37Rv_KO_CtpC	0.467	2.69
H37Rv_KO_CtpD	-0.907	-2.104
H37Rv_KO_Rv1272	0.341	2.043
H37Rv_KO_SugABC	0.902	2.4
H37Rv_KO_MbtN	0.392	0.369
Trans05	0.557	1.844
macrophage_unactivated	0.107	0.969
IL1	-0.739	-1.157
Rapamycin	-0.681	-0.902
Tcell	0.694	2.805
GMCSF	-1.117	-1.912
IFNab	-0.593	-1.826
IFNg	-1.384	-1.462
IFNg_GMCSF1	-1.628	-3.026
Rv1432_day32	-0.55	-0.583
Rv1565c_day32	0.175	0.0
secA2_input	-0.188	2.129
delta_Rv3594	-0.249	0.069
delta_Rv3717	0.371	1.576
delta_Rv3811	-0.665	-2.357
delta_Rv0954	0.813	-1.096
PonA1	0.726	-0.56
EccD1_KO	-0.276	-0.148
EspI_KO	0.262	-1.246
PE35_KO	0.379	1.275
PPE68_KO	0.534	1.238
glycerol2	1.188	4.047
lignocerate	1.47	4.212
oleate	0.387	0.0
phosphatidylcholine	1.27	3.961
acetate	1.549	5.772
glucAc	1.226	4.399
Rv0950ko	0.856	-0.742
Rv1096ko	0.32	-0.401
Rv3684ko	0.534	-0.141
delta_otsA_trehalose	1.077	-1.452