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 Rv2656c/-:

update plot	correlation	link to info on gene
Rv2330c/lppP	(cc=0.566)	info on Rv2330c/lppP
Rv2118c/-	(cc=0.5592)	info on Rv2118c/-
Rv2723/-	(cc=0.5565)	info on Rv2723/-
Rv0814c/sseC2	(cc=0.5387)	info on Rv0814c/sseC2
Rv1072/-	(cc=0.5011)	info on Rv1072/-
Rv0823c/-	(cc=0.4983)	info on Rv0823c/-
Rv3419c/gcp	(cc=0.4946)	info on Rv3419c/gcp
Rv2161c/-	(cc=0.4783)	info on Rv2161c/-
Rv2500c/fadE19	(cc=0.475)	info on Rv2500c/fadE19
Rv2398c/cysW	(cc=0.4733)	info on Rv2398c/cysW

Correlation of Rv2656c/- with Rv2330c/lppP

Normalized LFCs for Rv2656c/-:
(description and provenance of datasets)

	Rv2656c/-	Rv2330c/lppP
Fe_supp_jason_reseq	-0.043	0.497
low_pH_jason_reseq	0.045	-1.479
NO_jason_reseq	1.738	-1.061
B6_jason_reseq	1.599	0.083
MHCII_jason_reseq	0.99	0.375
Isoniazid02	0.354	0.343
Rifampicin4	0.39	0.639
Ethambutol3	2.977	1.245
Meropenem3	0.139	0.234
Vancomycin16	0.04	0.042
Rv2680_day32	0.658	0.111
H37Rv_KO_MarP	0.107	0.47
hypoxia_3wks	-0.801	-0.251
hypoxia_6wks	0.121	-0.416
glycerol	1.04	0.355
cholesterol	0.209	0.485
AJ	1.768	0.491
Bibs02	0.042	-0.04
Bibs02c	-0.221	0.023
BL6	0.18	1.646
BL6a	0.573	0.976
BXD01	1.882	0.144
BXD010	1.409	0.57
BXD011	2.756	1.203
BXD03	1.517	1.34
BXD04	2.194	0.173
BXD05	2.084	1.602
BXD06	1.44	1.19
BXD07	1.547	1.372
BXD08	1.072	0.949
BXD09	1.736	1.055
CAST	3.48	0.789
CCcont	0.606	1.074
DS01	0.108	0.075
DS02	0.099	-0.898
DS04	1.158	0.306
DS0c	1.023	0.0
GP01	-0.707	-0.077
GP02	-1.661	-1.576
GP0c	-0.291	-0.942
NOD	1.103	0.571
NZO	1.699	0.163
PWK	1.8	0.817
H37Rv_KO_CtpC	2.318	1.194
H37Rv_KO_CtpD	1.646	-0.319
H37Rv_KO_Rv1272	1.626	1.553
H37Rv_KO_SugABC	1.237	2.077
H37Rv_KO_MbtN	-0.55	-0.332
Trans05	2.493	1.858
macrophage_unactivated	0.347	-0.142
IL1	1.593	0.0
Rapamycin	0.534	0.325
Tcell	0.541	-1.414
GMCSF	0.158	0.385
IFNab	1.058	0.32
IFNg	1.371	0.698
IFNg_GMCSF1	1.207	0.069
Rv1432_day32	0.207	0.991
Rv1565c_day32	0.054	-0.728
secA2_input	1.119	1.057
delta_Rv3594	-0.974	-0.99
delta_Rv3717	-1.013	-1.217
delta_Rv3811	-1.423	-1.945
delta_Rv0954	-0.204	0.102
PonA1	-0.652	-0.13
EccD1_KO	2.345	-0.155
EspI_KO	0.416	-0.228
PE35_KO	0.201	-0.09
PPE68_KO	1.449	0.288
glycerol2	-0.168	0.247
lignocerate	0.472	0.69
oleate	-0.841	0.975
phosphatidylcholine	0.123	0.406
acetate	0.806	1.252
glucAc	0.641	0.49
Rv0950ko	-0.259	-1.731
Rv1096ko	-1.258	-0.452
Rv3684ko	-1.087	-0.632
delta_otsA_trehalose	0.114	-1.348