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 Rv0235c/-

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

	Rv1366/-	Rv0235c/-
Fe_supp_jason_reseq	-0.884	-0.783
low_pH_jason_reseq	-0.172	-0.204
NO_jason_reseq	-0.294	0.0
B6_jason_reseq	-0.871	-0.687
MHCII_jason_reseq	-0.267	-0.63
Isoniazid02	0.148	0.164
Rifampicin4	-0.376	0.0
Ethambutol3	0.269	0.035
Meropenem3	0.237	0.035
Vancomycin16	0.172	0.0
Rv2680_day32	-0.969	0.105
H37Rv_KO_MarP	0.518	0.155
hypoxia_3wks	-0.235	0.191
hypoxia_6wks	-0.048	-0.443
glycerol	-0.78	0.075
cholesterol	-0.44	-0.055
AJ	0.134	0.086
Bibs02	-0.823	-1.13
Bibs02c	0.656	0.039
BL6	0.376	1.27
BL6a	0.397	1.072
BXD01	0.834	1.126
BXD010	1.115	0.904
BXD011	0.35	0.508
BXD03	-0.278	1.42
BXD04	0.315	1.098
BXD05	0.231	0.447
BXD06	0.323	0.863
BXD07	0.476	1.406
BXD08	0.506	0.874
BXD09	-0.012	0.578
CAST	-0.142	0.205
CCcont	0.646	1.15
DS01	0.301	0.044
DS02	-0.254	-0.082
DS04	0.263	0.394
DS0c	0.525	-0.041
GP01	1.227	1.319
GP02	1.296	2.076
GP0c	0.54	0.788
NOD	0.148	0.866
NZO	0.839	0.212
PWK	0.406	0.571
H37Rv_KO_CtpC	0.467	1.221
H37Rv_KO_CtpD	-0.907	-0.661
H37Rv_KO_Rv1272	0.341	0.451
H37Rv_KO_SugABC	0.902	1.891
H37Rv_KO_MbtN	0.392	0.462
Trans05	0.557	1.231
macrophage_unactivated	0.107	0.805
IL1	-0.739	0.0
Rapamycin	-0.681	-0.592
Tcell	0.694	0.209
GMCSF	-1.117	0.708
IFNab	-0.593	-0.756
IFNg	-1.384	-0.775
IFNg_GMCSF1	-1.628	-0.666
Rv1432_day32	-0.55	1.25
Rv1565c_day32	0.175	0.0
secA2_input	-0.188	-0.031
delta_Rv3594	-0.249	0.909
delta_Rv3717	0.371	0.893
delta_Rv3811	-0.665	0.721
delta_Rv0954	0.813	0.699
PonA1	0.726	0.278
EccD1_KO	-0.276	0.0
EspI_KO	0.262	-0.419
PE35_KO	0.379	-0.28
PPE68_KO	0.534	0.099
glycerol2	1.188	1.1
lignocerate	1.47	0.956
oleate	0.387	0.719
phosphatidylcholine	1.27	0.634
acetate	1.549	0.459
glucAc	1.226	1.092
Rv0950ko	0.856	-0.292
Rv1096ko	0.32	-0.048
Rv3684ko	0.534	-0.373
delta_otsA_trehalose	1.077	-1.372