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 Rv1664/pks9

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

	Rv1729c/-	Rv1664/pks9
Fe_supp_jason_reseq	0.158	0.611
low_pH_jason_reseq	0.673	0.045
NO_jason_reseq	0.197	0.142
B6_jason_reseq	-0.947	-0.828
MHCII_jason_reseq	-1.6	-0.823
Isoniazid02	0.41	-0.615
Rifampicin4	0.103	0.317
Ethambutol3	2.122	-0.916
Meropenem3	0.45	-0.43
Vancomycin16	0.748	-0.066
Rv2680_day32	0.659	-0.348
H37Rv_KO_MarP	0.667	0.185
hypoxia_3wks	0.427	0.1
hypoxia_6wks	-0.159	-0.109
glycerol	0.686	0.835
cholesterol	-0.398	0.203
AJ	-0.297	-0.294
Bibs02	-1.183	-0.642
Bibs02c	-0.467	-0.735
BL6	1.501	0.357
BL6a	0.673	0.426
BXD01	0.48	0.843
BXD010	1.79	0.699
BXD011	1.392	0.761
BXD03	1.691	0.258
BXD04	1.224	0.914
BXD05	1.199	1.375
BXD06	1.382	0.775
BXD07	1.552	0.961
BXD08	1.23	0.75
BXD09	1.475	0.524
CAST	-0.095	-0.215
CCcont	1.406	0.618
DS01	-0.197	0.33
DS02	0.4	0.246
DS04	0.873	0.597
DS0c	0.248	0.717
GP01	1.093	1.902
GP02	0.064	-0.078
GP0c	1.136	0.564
NOD	-0.864	-0.21
NZO	-0.445	-0.061
PWK	-0.438	-0.315
H37Rv_KO_CtpC	1.041	0.828
H37Rv_KO_CtpD	0.502	1.22
H37Rv_KO_Rv1272	2.178	1.456
H37Rv_KO_SugABC	1.968	1.39
H37Rv_KO_MbtN	0.827	0.294
Trans05	2.694	1.335
macrophage_unactivated	1.108	0.997
IL1	2.186	0.866
Rapamycin	0.976	1.182
Tcell	0.635	1.105
GMCSF	1.217	1.017
IFNab	1.439	0.955
IFNg	0.938	0.906
IFNg_GMCSF1	0.317	0.525
Rv1432_day32	0.0	-0.142
Rv1565c_day32	0.951	0.531
secA2_input	-1.442	-0.65
delta_Rv3594	-0.196	-0.311
delta_Rv3717	-0.751	-1.008
delta_Rv3811	-0.19	-0.47
delta_Rv0954	-0.678	-0.74
PonA1	-0.733	-0.744
EccD1_KO	-1.223	-0.549
EspI_KO	0.183	-0.935
PE35_KO	1.015	-0.563
PPE68_KO	1.277	-0.454
glycerol2	-0.727	-0.862
lignocerate	-0.632	-0.721
oleate	-0.421	-0.364
phosphatidylcholine	-0.597	-0.623
acetate	0.264	-0.806
glucAc	0.164	-0.808
Rv0950ko	0.694	-0.371
Rv1096ko	1.475	0.277
Rv3684ko	-0.789	-0.665
delta_otsA_trehalose	-0.778	1.396