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 Rv1740/vapB34:

update plot	correlation	link to info on gene
Rv2268c/cyp128	(cc=0.3936)	info on Rv2268c/cyp128
Rv1718/-	(cc=0.3894)	info on Rv1718/-
Rv3780/-	(cc=0.3799)	info on Rv3780/-
Rv1371/-	(cc=0.3714)	info on Rv1371/-
Rv2896c/-	(cc=0.3707)	info on Rv2896c/-
Rv3453/-	(cc=0.3697)	info on Rv3453/-
Rv2657c/-	(cc=0.3586)	info on Rv2657c/-
Rv0338c/-	(cc=0.3581)	info on Rv0338c/-
Rv0093c/-	(cc=0.3462)	info on Rv0093c/-
Rv1805c/-	(cc=0.3444)	info on Rv1805c/-

Correlation of Rv1740/vapB34 with Rv2268c/cyp128

Normalized LFCs for Rv1740/vapB34:
(description and provenance of datasets)

	Rv1740/vapB34	Rv2268c/cyp128
Fe_supp_jason_reseq	-0.079	-0.906
low_pH_jason_reseq	-0.214	-0.196
NO_jason_reseq	0.648	-0.714
B6_jason_reseq	1.395	-0.834
MHCII_jason_reseq	0.564	-1.068
Isoniazid02	-0.099	-0.105
Rifampicin4	0.211	-0.298
Ethambutol3	-0.32	-0.134
Meropenem3	0.436	0.875
Vancomycin16	0.0	0.0
Rv2680_day32	-0.116	-0.874
H37Rv_KO_MarP	0.467	-0.11
hypoxia_3wks	-0.726	-0.518
hypoxia_6wks	-0.38	-0.161
glycerol	0.338	1.434
cholesterol	3.968	6.0
AJ	1.321	0.632
Bibs02	0.134	0.792
Bibs02c	0.43	1.299
BL6	-1.089	1.26
BL6a	-0.547	0.623
BXD01	-0.103	0.489
BXD010	-1.592	0.0
BXD011	-0.661	0.29
BXD03	-1.379	1.271
BXD04	2.124	-0.408
BXD05	0.891	0.814
BXD06	-0.219	0.334
BXD07	0.608	0.377
BXD08	0.306	0.648
BXD09	-0.043	0.527
CAST	0.964	1.039
CCcont	0.171	0.082
DS01	-0.072	0.065
DS02	0.843	1.022
DS04	-0.059	-1.248
DS0c	1.453	1.095
GP01	-1.007	-0.802
GP02	1.771	1.79
GP0c	0.095	-0.836
NOD	1.822	1.595
NZO	1.779	1.329
PWK	-1.223	0.108
H37Rv_KO_CtpC	1.307	-0.473
H37Rv_KO_CtpD	1.121	1.684
H37Rv_KO_Rv1272	0.815	1.022
H37Rv_KO_SugABC	-1.513	1.209
H37Rv_KO_MbtN	0.399	0.933
Trans05	0.947	0.982
macrophage_unactivated	0.382	-0.354
IL1	1.907	0.308
Rapamycin	-0.58	-0.718
Tcell	0.241	0.45
GMCSF	0.132	0.774
IFNab	0.505	-0.707
IFNg	1.676	-0.299
IFNg_GMCSF1	-2.212	-0.735
Rv1432_day32	1.37	0.287
Rv1565c_day32	-1.69	0.602
secA2_input	0.144	-0.146
delta_Rv3594	1.078	0.912
delta_Rv3717	0.656	0.0
delta_Rv3811	0.623	0.049
delta_Rv0954	-0.861	-0.23
PonA1	0.267	-0.039
EccD1_KO	-2.424	-1.059
EspI_KO	-0.479	-0.168
PE35_KO	0.732	0.904
PPE68_KO	1.315	0.442
glycerol2	0.999	0.144
lignocerate	1.946	-0.346
oleate	-2.083	-0.483
phosphatidylcholine	0.744	-0.132
acetate	1.696	-0.183
glucAc	1.61	-0.565
Rv0950ko	0.832	-0.808
Rv1096ko	0.715	-0.808
Rv3684ko	0.819	-0.783
delta_otsA_trehalose	-0.897	-0.838