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 Rv1551/plsB1

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

	Rv1729c/-	Rv1551/plsB1
Fe_supp_jason_reseq	0.158	0.923
low_pH_jason_reseq	0.673	-0.266
NO_jason_reseq	0.197	-0.079
B6_jason_reseq	-0.947	-1.362
MHCII_jason_reseq	-1.6	-0.572
Isoniazid02	0.41	-0.127
Rifampicin4	0.103	-0.799
Ethambutol3	2.122	-0.186
Meropenem3	0.45	0.818
Vancomycin16	0.748	-0.164
Rv2680_day32	0.659	-0.362
H37Rv_KO_MarP	0.667	-0.041
hypoxia_3wks	0.427	0.467
hypoxia_6wks	-0.159	0.501
glycerol	0.686	0.0
cholesterol	-0.398	0.54
AJ	-0.297	0.471
Bibs02	-1.183	-0.216
Bibs02c	-0.467	0.077
BL6	1.501	1.452
BL6a	0.673	1.027
BXD01	0.48	0.776
BXD010	1.79	0.664
BXD011	1.392	1.181
BXD03	1.691	0.654
BXD04	1.224	1.037
BXD05	1.199	0.698
BXD06	1.382	0.992
BXD07	1.552	1.126
BXD08	1.23	0.874
BXD09	1.475	1.168
CAST	-0.095	-0.043
CCcont	1.406	0.858
DS01	-0.197	0.368
DS02	0.4	0.474
DS04	0.873	0.846
DS0c	0.248	0.662
GP01	1.093	1.403
GP02	0.064	2.109
GP0c	1.136	1.501
NOD	-0.864	-0.085
NZO	-0.445	-0.114
PWK	-0.438	-0.037
H37Rv_KO_CtpC	1.041	1.161
H37Rv_KO_CtpD	0.502	0.714
H37Rv_KO_Rv1272	2.178	1.832
H37Rv_KO_SugABC	1.968	1.585
H37Rv_KO_MbtN	0.827	1.287
Trans05	2.694	1.442
macrophage_unactivated	1.108	0.29
IL1	2.186	0.602
Rapamycin	0.976	1.169
Tcell	0.635	0.85
GMCSF	1.217	0.473
IFNab	1.439	0.925
IFNg	0.938	0.786
IFNg_GMCSF1	0.317	0.487
Rv1432_day32	0.0	-0.587
Rv1565c_day32	0.951	0.665
secA2_input	-1.442	-0.983
delta_Rv3594	-0.196	0.433
delta_Rv3717	-0.751	0.371
delta_Rv3811	-0.19	-0.284
delta_Rv0954	-0.678	0.366
PonA1	-0.733	0.669
EccD1_KO	-1.223	0.043
EspI_KO	0.183	0.724
PE35_KO	1.015	0.508
PPE68_KO	1.277	0.557
glycerol2	-0.727	-0.147
lignocerate	-0.632	0.035
oleate	-0.421	0.322
phosphatidylcholine	-0.597	0.265
acetate	0.264	0.095
glucAc	0.164	-0.124
Rv0950ko	0.694	-0.356
Rv1096ko	1.475	0.112
Rv3684ko	-0.789	0.121
delta_otsA_trehalose	-0.778	0.34