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 Rv3691/-

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

	Rv3312A/-	Rv3691/-
Fe_supp_jason_reseq	-0.35	-0.56
low_pH_jason_reseq	-0.132	-1.437
NO_jason_reseq	0.893	-0.302
B6_jason_reseq	1.266	-0.063
MHCII_jason_reseq	0.295	-0.313
Isoniazid02	0.941	-0.146
Rifampicin4	0.742	0.49
Ethambutol3	0.548	1.235
Meropenem3	2.13	1.636
Vancomycin16	0.727	0.663
Rv2680_day32	-0.959	-0.458
H37Rv_KO_MarP	0.344	-0.751
hypoxia_3wks	-0.231	0.247
hypoxia_6wks	-0.395	0.098
glycerol	0.726	-1.221
cholesterol	0.382	0.295
AJ	0.225	0.563
Bibs02	-1.288	-0.462
Bibs02c	-0.975	0.409
BL6	-0.038	-1.048
BL6a	-0.436	0.131
BXD01	0.434	0.404
BXD010	-0.436	-0.819
BXD011	-0.098	-0.438
BXD03	0.181	-0.376
BXD04	-0.474	-0.392
BXD05	0.265	-0.911
BXD06	0.331	-0.108
BXD07	0.75	-0.173
BXD08	-0.034	0.931
BXD09	0.066	-0.1
CAST	-0.017	1.043
CCcont	0.157	-0.378
DS01	-0.27	0.481
DS02	0.274	0.477
DS04	0.022	0.891
DS0c	0.064	0.388
GP01	0.31	0.065
GP02	1.1	-0.221
GP0c	0.597	0.521
NOD	0.382	0.384
NZO	-0.377	-0.205
PWK	-0.328	1.89
H37Rv_KO_CtpC	-0.717	-0.332
H37Rv_KO_CtpD	0.144	0.083
H37Rv_KO_Rv1272	-0.912	-0.878
H37Rv_KO_SugABC	-0.312	0.336
H37Rv_KO_MbtN	0.777	-0.287
Trans05	-0.372	0.396
macrophage_unactivated	0.133	-0.363
IL1	0.113	-1.373
Rapamycin	0.292	-0.098
Tcell	0.336	0.052
GMCSF	-0.034	-0.127
IFNab	-0.804	0.048
IFNg	0.551	-0.128
IFNg_GMCSF1	-0.478	-0.258
Rv1432_day32	0.48	0.905
Rv1565c_day32	-3.838	-1.579
secA2_input	0.243	0.366
delta_Rv3594	1.41	0.226
delta_Rv3717	1.221	0.769
delta_Rv3811	0.55	0.193
delta_Rv0954	1.469	0.446
PonA1	1.13	1.108
EccD1_KO	-0.747	-0.947
EspI_KO	-0.374	-0.821
PE35_KO	-0.875	-1.047
PPE68_KO	-0.771	-1.104
glycerol2	1.241	1.297
lignocerate	1.444	1.033
oleate	0.771	1.935
phosphatidylcholine	1.408	0.95
acetate	0.48	1.476
glucAc	0.764	0.701
Rv0950ko	0.519	0.0
Rv1096ko	0.452	0.878
Rv3684ko	0.252	0.76
delta_otsA_trehalose	-0.354	0.876