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 Rv3312A/-:

update plot	correlation	link to info on gene
Rv1680/-	(cc=0.5035)	info on Rv1680/-
Rv3691/-	(cc=0.4858)	info on Rv3691/-
Rv3703c/-	(cc=0.4702)	info on Rv3703c/-
Rv3395c/-	(cc=0.4565)	info on Rv3395c/-
Rv3256c/-	(cc=0.4528)	info on Rv3256c/-
Rv3836/-	(cc=0.4501)	info on Rv3836/-
Rv2404c/lepA	(cc=0.447)	info on Rv2404c/lepA
Rv2583c/relA	(cc=0.4342)	info on Rv2583c/relA
Rv1569/bioF1	(cc=0.4332)	info on Rv1569/bioF1
Rv1558/-	(cc=0.4323)	info on Rv1558/-

Correlation of Rv3312A/- with Rv3836/-

Normalized LFCs for Rv3312A/-:
(description and provenance of datasets)

	Rv3312A/-	Rv3836/-
Fe_supp_jason_reseq	-0.35	-1.32
low_pH_jason_reseq	-0.132	-0.793
NO_jason_reseq	0.893	0.685
B6_jason_reseq	1.266	-0.122
MHCII_jason_reseq	0.295	-0.063
Isoniazid02	0.941	0.287
Rifampicin4	0.742	0.122
Ethambutol3	0.548	0.295
Meropenem3	2.13	0.401
Vancomycin16	0.727	0.175
Rv2680_day32	-0.959	-0.335
H37Rv_KO_MarP	0.344	1.054
hypoxia_3wks	-0.231	0.279
hypoxia_6wks	-0.395	-0.612
glycerol	0.726	-0.026
cholesterol	0.382	0.115
AJ	0.225	0.116
Bibs02	-1.288	0.844
Bibs02c	-0.975	0.276
BL6	-0.038	0.273
BL6a	-0.436	0.522
BXD01	0.434	0.437
BXD010	-0.436	0.161
BXD011	-0.098	0.427
BXD03	0.181	0.49
BXD04	-0.474	-0.195
BXD05	0.265	0.772
BXD06	0.331	0.69
BXD07	0.75	-0.072
BXD08	-0.034	0.337
BXD09	0.066	0.398
CAST	-0.017	0.584
CCcont	0.157	0.689
DS01	-0.27	-0.062
DS02	0.274	0.041
DS04	0.022	-0.923
DS0c	0.064	-0.544
GP01	0.31	-0.085
GP02	1.1	1.926
GP0c	0.597	0.746
NOD	0.382	-0.163
NZO	-0.377	1.458
PWK	-0.328	0.202
H37Rv_KO_CtpC	-0.717	0.46
H37Rv_KO_CtpD	0.144	0.048
H37Rv_KO_Rv1272	-0.912	0.561
H37Rv_KO_SugABC	-0.312	1.408
H37Rv_KO_MbtN	0.777	0.088
Trans05	-0.372	-0.416
macrophage_unactivated	0.133	0.0
IL1	0.113	0.973
Rapamycin	0.292	0.258
Tcell	0.336	0.199
GMCSF	-0.034	0.393
IFNab	-0.804	-0.45
IFNg	0.551	-0.468
IFNg_GMCSF1	-0.478	-0.305
Rv1432_day32	0.48	0.078
Rv1565c_day32	-3.838	-2.889
secA2_input	0.243	0.723
delta_Rv3594	1.41	-0.531
delta_Rv3717	1.221	0.167
delta_Rv3811	0.55	0.238
delta_Rv0954	1.469	0.0
PonA1	1.13	0.422
EccD1_KO	-0.747	-1.273
EspI_KO	-0.374	-0.964
PE35_KO	-0.875	-0.662
PPE68_KO	-0.771	-0.889
glycerol2	1.241	1.037
lignocerate	1.444	0.975
oleate	0.771	0.683
phosphatidylcholine	1.408	0.675
acetate	0.48	0.366
glucAc	0.764	0.118
Rv0950ko	0.519	-0.555
Rv1096ko	0.452	-0.579
Rv3684ko	0.252	-1.503
delta_otsA_trehalose	-0.354	-0.871