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 Rv1891/-

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

	Rv1729c/-	Rv1891/-
Fe_supp_jason_reseq	0.158	0.152
low_pH_jason_reseq	0.673	0.182
NO_jason_reseq	0.197	-0.58
B6_jason_reseq	-0.947	-1.736
MHCII_jason_reseq	-1.6	-2.1
Isoniazid02	0.41	-0.856
Rifampicin4	0.103	-0.436
Ethambutol3	2.122	-1.052
Meropenem3	0.45	-0.55
Vancomycin16	0.748	0.013
Rv2680_day32	0.659	0.038
H37Rv_KO_MarP	0.667	0.416
hypoxia_3wks	0.427	-0.072
hypoxia_6wks	-0.159	-1.194
glycerol	0.686	0.148
cholesterol	-0.398	-0.331
AJ	-0.297	1.151
Bibs02	-1.183	-2.375
Bibs02c	-0.467	-0.534
BL6	1.501	0.932
BL6a	0.673	1.036
BXD01	0.48	1.005
BXD010	1.79	0.766
BXD011	1.392	0.785
BXD03	1.691	1.371
BXD04	1.224	-0.082
BXD05	1.199	0.39
BXD06	1.382	0.93
BXD07	1.552	1.317
BXD08	1.23	1.423
BXD09	1.475	1.202
CAST	-0.095	0.389
CCcont	1.406	1.191
DS01	-0.197	-0.736
DS02	0.4	0.326
DS04	0.873	0.103
DS0c	0.248	-0.553
GP01	1.093	0.477
GP02	0.064	1.328
GP0c	1.136	1.587
NOD	-0.864	0.208
NZO	-0.445	1.017
PWK	-0.438	0.0
H37Rv_KO_CtpC	1.041	1.865
H37Rv_KO_CtpD	0.502	0.924
H37Rv_KO_Rv1272	2.178	0.869
H37Rv_KO_SugABC	1.968	0.657
H37Rv_KO_MbtN	0.827	1.416
Trans05	2.694	1.462
macrophage_unactivated	1.108	0.615
IL1	2.186	-0.394
Rapamycin	0.976	0.246
Tcell	0.635	-0.355
GMCSF	1.217	0.116
IFNab	1.439	0.747
IFNg	0.938	0.158
IFNg_GMCSF1	0.317	-0.575
Rv1432_day32	0.0	-0.022
Rv1565c_day32	0.951	0.379
secA2_input	-1.442	0.063
delta_Rv3594	-0.196	0.102
delta_Rv3717	-0.751	-0.072
delta_Rv3811	-0.19	-1.029
delta_Rv0954	-0.678	-0.662
PonA1	-0.733	-0.19
EccD1_KO	-1.223	-0.26
EspI_KO	0.183	0.334
PE35_KO	1.015	-0.193
PPE68_KO	1.277	-0.522
glycerol2	-0.727	-0.446
lignocerate	-0.632	-0.409
oleate	-0.421	-0.489
phosphatidylcholine	-0.597	-0.598
acetate	0.264	-0.218
glucAc	0.164	-0.234
Rv0950ko	0.694	0.724
Rv1096ko	1.475	0.368
Rv3684ko	-0.789	0.0
delta_otsA_trehalose	-0.778	-0.84