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 Rv3304/-:

update plot	correlation	link to info on gene
Rv2645/-	(cc=0.4444)	info on Rv2645/-
Rv3777/-	(cc=0.4319)	info on Rv3777/-
Rv3463/-	(cc=0.4139)	info on Rv3463/-
Rv2334/cysK1	(cc=0.3777)	info on Rv2334/cysK1
Rv0302/-	(cc=0.3773)	info on Rv0302/-
Rv2232/ptkA	(cc=0.3741)	info on Rv2232/ptkA
Rv2571c/-	(cc=0.3738)	info on Rv2571c/-
Rv0695/-	(cc=0.3659)	info on Rv0695/-
Rv1033c/trcR	(cc=0.3617)	info on Rv1033c/trcR
Rv0927c/-	(cc=0.3591)	info on Rv0927c/-

Correlation of Rv3304/- with Rv2334/cysK1

Normalized LFCs for Rv3304/-:
(description and provenance of datasets)

	Rv3304/-	Rv2334/cysK1
Fe_supp_jason_reseq	0.35	2.437
low_pH_jason_reseq	1.206	5.069
NO_jason_reseq	-1.137	1.089
B6_jason_reseq	-0.123	0.357
MHCII_jason_reseq	-0.026	-0.257
Isoniazid02	0.982	3.403
Rifampicin4	-2.28	0.634
Ethambutol3	0.0	0.285
Meropenem3	-0.636	-0.335
Vancomycin16	-0.817	0.809
Rv2680_day32	0.131	0.0
H37Rv_KO_MarP	1.659	1.666
hypoxia_3wks	0.0	-1.284
hypoxia_6wks	1.054	0.378
glycerol	0.651	2.455
cholesterol	-1.453	1.761
AJ	0.931	0.232
Bibs02	0.335	0.0
Bibs02c	0.674	0.0
BL6	-0.725	0.53
BL6a	0.994	1.435
BXD01	0.057	2.245
BXD010	1.198	1.115
BXD011	-0.088	0.626
BXD03	0.392	1.351
BXD04	0.027	1.184
BXD05	-0.888	1.109
BXD06	0.058	1.485
BXD07	-0.095	0.768
BXD08	0.992	2.419
BXD09	0.334	0.863
CAST	-0.27	3.337
CCcont	0.274	1.492
DS01	1.519	0.45
DS02	0.477	0.217
DS04	0.0	0.37
DS0c	-0.049	0.0
GP01	-0.045	0.0
GP02	-1.117	0.0
GP0c	-0.253	0.0
NOD	-0.208	1.507
NZO	0.087	0.0
PWK	-0.99	0.196
H37Rv_KO_CtpC	-0.706	0.0
H37Rv_KO_CtpD	-1.199	0.703
H37Rv_KO_Rv1272	-0.477	0.269
H37Rv_KO_SugABC	0.064	0.664
H37Rv_KO_MbtN	-1.23	0.283
Trans05	-0.976	0.803
macrophage_unactivated	-0.496	0.398
IL1	-1.317	-0.409
Rapamycin	-2.133	-0.424
Tcell	-0.668	-0.45
GMCSF	-1.489	0.0
IFNab	0.369	-0.417
IFNg	-2.143	-0.369
IFNg_GMCSF1	-1.395	0.0
Rv1432_day32	-0.035	-0.18
Rv1565c_day32	-1.085	1.507
secA2_input	0.186	-1.315
delta_Rv3594	-1.265	-2.522
delta_Rv3717	-1.36	-2.896
delta_Rv3811	-1.692	-2.767
delta_Rv0954	-1.129	-0.716
PonA1	-0.41	0.864
EccD1_KO	0.174	0.526
EspI_KO	0.299	2.053
PE35_KO	0.922	0.683
PPE68_KO	1.081	1.59
glycerol2	2.089	-1.208
lignocerate	0.065	-0.756
oleate	0.149	-1.418
phosphatidylcholine	0.111	-1.401
acetate	-2.59	0.72
glucAc	-1.61	0.272
Rv0950ko	0.874	1.999
Rv1096ko	2.542	2.925
Rv3684ko	0.147	2.044
delta_otsA_trehalose	0.065	0.854