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 Rv2019/-:

update plot	correlation	link to info on gene
Rv2237/-	(cc=0.6506)	info on Rv2237/-
Rv2008c/-	(cc=0.6496)	info on Rv2008c/-
Rv1289/-	(cc=0.6429)	info on Rv1289/-
Rv2550c/vapB20	(cc=0.6143)	info on Rv2550c/vapB20
Rv0488/-	(cc=0.6115)	info on Rv0488/-
Rv0789c/-	(cc=0.6029)	info on Rv0789c/-
Rv2119/-	(cc=0.6019)	info on Rv2119/-
Rv2237A/-	(cc=0.596)	info on Rv2237A/-
Rv0963c/-	(cc=0.5944)	info on Rv0963c/-
Rv1489A/-	(cc=0.5773)	info on Rv1489A/-

Correlation of Rv2019/- with Rv0963c/-

Normalized LFCs for Rv2019/-:
(description and provenance of datasets)

	Rv2019/-	Rv0963c/-
Fe_supp_jason_reseq	0.44	-0.998
low_pH_jason_reseq	-0.156	-1.031
NO_jason_reseq	-0.013	-0.081
B6_jason_reseq	0.823	0.652
MHCII_jason_reseq	0.456	-0.415
Isoniazid02	0.118	0.113
Rifampicin4	0.325	-0.479
Ethambutol3	-0.124	-0.308
Meropenem3	0.059	-0.108
Vancomycin16	0.273	0.47
Rv2680_day32	0.594	-0.045
H37Rv_KO_MarP	-0.807	0.532
hypoxia_3wks	-0.845	-1.587
hypoxia_6wks	0.578	-0.831
glycerol	-0.512	-0.594
cholesterol	0.244	-0.226
AJ	-0.373	0.419
Bibs02	-0.021	0.585
Bibs02c	-0.635	0.068
BL6	-0.386	0.424
BL6a	-0.093	0.102
BXD01	-0.498	-0.869
BXD010	0.09	0.042
BXD011	0.606	0.042
BXD03	-0.532	-0.352
BXD04	-0.494	-0.28
BXD05	0.324	-0.372
BXD06	0.065	0.06
BXD07	-0.054	-0.791
BXD08	-0.214	0.118
BXD09	0.063	-0.307
CAST	-0.584	0.339
CCcont	0.671	0.132
DS01	0.474	0.18
DS02	0.517	-0.458
DS04	0.822	-0.132
DS0c	-0.702	0.896
GP01	-0.629	-0.789
GP02	-0.134	-0.237
GP0c	0.009	-0.7
NOD	0.068	0.918
NZO	-0.046	0.35
PWK	0.044	0.398
H37Rv_KO_CtpC	0.085	0.727
H37Rv_KO_CtpD	-0.333	0.186
H37Rv_KO_Rv1272	1.223	0.316
H37Rv_KO_SugABC	0.041	0.273
H37Rv_KO_MbtN	1.693	0.146
Trans05	1.087	0.456
macrophage_unactivated	-0.83	-0.716
IL1	-0.222	-0.077
Rapamycin	0.187	-0.362
Tcell	0.182	-0.978
GMCSF	0.121	0.937
IFNab	0.632	-0.475
IFNg	-0.444	-0.446
IFNg_GMCSF1	-0.468	-1.442
Rv1432_day32	0.055	-0.67
Rv1565c_day32	0.57	0.215
secA2_input	-1.367	-0.379
delta_Rv3594	0.838	0.694
delta_Rv3717	-0.186	0.35
delta_Rv3811	0.697	0.162
delta_Rv0954	-0.151	-0.152
PonA1	-0.492	-0.108
EccD1_KO	0.927	0.345
EspI_KO	1.03	0.71
PE35_KO	1.52	0.636
PPE68_KO	1.369	-0.029
glycerol2	2.299	1.342
lignocerate	2.763	2.081
oleate	-0.062	-0.296
phosphatidylcholine	2.346	1.342
acetate	3.72	2.103
glucAc	2.122	2.008
Rv0950ko	0.748	0.832
Rv1096ko	-0.461	1.062
Rv3684ko	-0.196	0.665
delta_otsA_trehalose	0.21	0.423