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 Rv1729c/-:

update plot	correlation	link to info on gene
Rv3398c/idsA1	(cc=0.6624)	info on Rv3398c/idsA1
Rv0844c/narL	(cc=0.6417)	info on Rv0844c/narL
Rv1664/pks9	(cc=0.6371)	info on Rv1664/pks9
Rv3759c/proX	(cc=0.5882)	info on Rv3759c/proX
Rv1021/-	(cc=0.5861)	info on Rv1021/-
Rv1551/plsB1	(cc=0.5828)	info on Rv1551/plsB1
Rv1616/-	(cc=0.5771)	info on Rv1616/-
Rv1891/-	(cc=0.5598)	info on Rv1891/-
Rv3146/nuoB	(cc=0.5528)	info on Rv3146/nuoB
Rv1870c/-	(cc=0.55)	info on Rv1870c/-

Correlation of Rv1729c/- with Rv3398c/idsA1

Normalized LFCs for Rv1729c/-:
(description and provenance of datasets)

	Rv1729c/-	Rv3398c/idsA1
Fe_supp_jason_reseq	0.158	-0.677
low_pH_jason_reseq	0.673	0.694
NO_jason_reseq	0.197	-0.11
B6_jason_reseq	-0.947	-2.06
MHCII_jason_reseq	-1.6	-2.841
Isoniazid02	0.41	2.012
Rifampicin4	0.103	-0.403
Ethambutol3	2.122	1.411
Meropenem3	0.45	-0.255
Vancomycin16	0.748	0.358
Rv2680_day32	0.659	0.041
H37Rv_KO_MarP	0.667	0.165
hypoxia_3wks	0.427	0.359
hypoxia_6wks	-0.159	0.748
glycerol	0.686	-1.229
cholesterol	-0.398	-0.24
AJ	-0.297	-1.287
Bibs02	-1.183	-0.303
Bibs02c	-0.467	-0.762
BL6	1.501	-0.208
BL6a	0.673	1.373
BXD01	0.48	1.355
BXD010	1.79	1.403
BXD011	1.392	1.139
BXD03	1.691	1.948
BXD04	1.224	1.608
BXD05	1.199	1.701
BXD06	1.382	1.245
BXD07	1.552	1.105
BXD08	1.23	1.062
BXD09	1.475	1.379
CAST	-0.095	-0.302
CCcont	1.406	0.173
DS01	-0.197	0.339
DS02	0.4	0.876
DS04	0.873	0.698
DS0c	0.248	-1.092
GP01	1.093	-0.164
GP02	0.064	0.722
GP0c	1.136	-1.112
NOD	-0.864	-0.07
NZO	-0.445	-0.062
PWK	-0.438	0.117
H37Rv_KO_CtpC	1.041	2.762
H37Rv_KO_CtpD	0.502	1.542
H37Rv_KO_Rv1272	2.178	2.022
H37Rv_KO_SugABC	1.968	2.161
H37Rv_KO_MbtN	0.827	0.0
Trans05	2.694	0.986
macrophage_unactivated	1.108	1.787
IL1	2.186	1.317
Rapamycin	0.976	1.406
Tcell	0.635	1.16
GMCSF	1.217	1.79
IFNab	1.439	1.427
IFNg	0.938	1.224
IFNg_GMCSF1	0.317	1.694
Rv1432_day32	0.0	0.85
Rv1565c_day32	0.951	1.591
secA2_input	-1.442	0.0
delta_Rv3594	-0.196	-0.436
delta_Rv3717	-0.751	-1.081
delta_Rv3811	-0.19	-0.998
delta_Rv0954	-0.678	-0.585
PonA1	-0.733	0.275
EccD1_KO	-1.223	-0.678
EspI_KO	0.183	0.61
PE35_KO	1.015	0.624
PPE68_KO	1.277	1.328
glycerol2	-0.727	-1.327
lignocerate	-0.632	-1.122
oleate	-0.421	0.22
phosphatidylcholine	-0.597	-0.896
acetate	0.264	-1.287
glucAc	0.164	-1.381
Rv0950ko	0.694	-0.06
Rv1096ko	1.475	1.04
Rv3684ko	-0.789	-0.4
delta_otsA_trehalose	-0.778	0.58