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 Rv0115/hddA:

update plot	correlation	link to info on gene
Rv0399c/lpqK	(cc=0.6841)	info on Rv0399c/lpqK
Rv0940c/-	(cc=0.6452)	info on Rv0940c/-
Rv0194/-	(cc=0.6193)	info on Rv0194/-
Rv1501/-	(cc=0.6143)	info on Rv1501/-
Rv0160c/PE4	(cc=0.5854)	info on Rv0160c/PE4
Rv0342/iniA	(cc=0.5757)	info on Rv0342/iniA
Rv3508/PE_PGRS54	(cc=0.5622)	info on Rv3508/PE_PGRS54
Rv3329/-	(cc=0.553)	info on Rv3329/-
Rv0343/iniC	(cc=0.5332)	info on Rv0343/iniC
Rv3191c/-	(cc=0.5259)	info on Rv3191c/-

Correlation of Rv0115/hddA with Rv1501/-

Normalized LFCs for Rv0115/hddA:
(description and provenance of datasets)

	Rv0115/hddA	Rv1501/-
Fe_supp_jason_reseq	-0.505	0.534
low_pH_jason_reseq	0.028	-0.284
NO_jason_reseq	0.478	0.0
B6_jason_reseq	0.344	0.357
MHCII_jason_reseq	0.484	1.169
Isoniazid02	-2.546	-1.711
Rifampicin4	0.495	0.523
Ethambutol3	-2.227	-2.135
Meropenem3	-1.848	-2.414
Vancomycin16	-0.921	-0.748
Rv2680_day32	0.104	0.594
H37Rv_KO_MarP	0.574	-0.267
hypoxia_3wks	0.152	0.104
hypoxia_6wks	0.906	0.457
glycerol	0.521	-0.11
cholesterol	0.021	-0.551
AJ	0.333	0.708
Bibs02	-0.864	0.354
Bibs02c	0.191	0.553
BL6	-0.218	-0.045
BL6a	0.453	-0.343
BXD01	0.17	-0.095
BXD010	0.323	-0.222
BXD011	-0.463	0.129
BXD03	0.159	0.549
BXD04	0.0	1.491
BXD05	0.0	0.797
BXD06	-0.165	0.07
BXD07	0.19	-0.424
BXD08	0.173	0.963
BXD09	0.128	0.465
CAST	-0.23	0.732
CCcont	0.064	-0.493
DS01	0.609	0.842
DS02	0.284	-0.039
DS04	0.489	-0.419
DS0c	-0.148	0.718
GP01	0.468	0.1
GP02	-0.338	-0.618
GP0c	0.469	0.11
NOD	-0.511	0.117
NZO	-0.136	0.555
PWK	0.594	0.068
H37Rv_KO_CtpC	-0.37	0.407
H37Rv_KO_CtpD	1.079	0.825
H37Rv_KO_Rv1272	0.109	0.655
H37Rv_KO_SugABC	1.569	1.084
H37Rv_KO_MbtN	-0.653	1.254
Trans05	0.575	0.363
macrophage_unactivated	0.11	0.956
IL1	-0.747	-0.584
Rapamycin	-0.709	-0.715
Tcell	0.417	0.652
GMCSF	-0.61	-0.338
IFNab	-0.514	-0.094
IFNg	0.139	-0.083
IFNg_GMCSF1	-0.694	-0.732
Rv1432_day32	0.029	0.188
Rv1565c_day32	-0.36	0.535
secA2_input	-0.517	-0.302
delta_Rv3594	-0.448	-0.684
delta_Rv3717	-0.96	-1.104
delta_Rv3811	-0.629	-0.665
delta_Rv0954	-0.366	0.021
PonA1	-0.806	-1.191
EccD1_KO	-1.246	-0.536
EspI_KO	-0.422	-0.168
PE35_KO	-0.627	-0.537
PPE68_KO	-0.659	-0.253
glycerol2	0.332	0.591
lignocerate	0.544	0.247
oleate	0.072	0.842
phosphatidylcholine	0.392	0.591
acetate	0.258	-0.14
glucAc	0.389	-0.117
Rv0950ko	0.241	-0.235
Rv1096ko	-0.642	-1.33
Rv3684ko	-1.055	-0.992
delta_otsA_trehalose	-0.019	-2.691