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 Rv0116c/ldtA:

update plot	correlation	link to info on gene
Rv2748c/ftsK	(cc=0.5142)	info on Rv2748c/ftsK
Rv2678c/hemE	(cc=0.4702)	info on Rv2678c/hemE
Rv2373c/dnaJ2	(cc=0.4691)	info on Rv2373c/dnaJ2
Rv3673c/-	(cc=0.4598)	info on Rv3673c/-
Rv0701/rplC	(cc=0.4575)	info on Rv0701/rplC
Rv3753c/-	(cc=0.4515)	info on Rv3753c/-
Rv0237/lpqI	(cc=0.4405)	info on Rv0237/lpqI
Rv2882c/frr	(cc=0.4315)	info on Rv2882c/frr
Rv3858c/gltD	(cc=0.4309)	info on Rv3858c/gltD
Rv2164c/-	(cc=0.4269)	info on Rv2164c/-

Correlation of Rv0116c/ldtA with Rv3753c/-

Normalized LFCs for Rv0116c/ldtA:
(description and provenance of datasets)

	Rv0116c/ldtA	Rv3753c/-
Fe_supp_jason_reseq	1.223	1.778
low_pH_jason_reseq	0.542	0.582
NO_jason_reseq	-0.953	-0.362
B6_jason_reseq	-0.136	-0.153
MHCII_jason_reseq	1.177	0.0
Isoniazid02	-0.944	0.0
Rifampicin4	-0.311	0.0
Ethambutol3	-0.423	0.0
Meropenem3	0.018	0.0
Vancomycin16	-0.923	0.0
Rv2680_day32	-0.459	0.0
H37Rv_KO_MarP	0.636	-0.255
hypoxia_3wks	0.12	0.0
hypoxia_6wks	-0.562	0.0
glycerol	-0.74	0.0
cholesterol	-0.43	0.0
AJ	0.329	0.0
Bibs02	0.139	0.0
Bibs02c	-0.288	0.0
BL6	0.473	0.0
BL6a	-0.187	0.0
BXD01	0.342	0.0
BXD010	-0.297	0.0
BXD011	-0.519	0.243
BXD03	0.336	0.0
BXD04	-0.304	1.619
BXD05	-0.07	0.0
BXD06	0.241	0.0
BXD07	0.0	0.0
BXD08	0.044	0.0
BXD09	0.077	0.0
CAST	0.063	0.0
CCcont	0.517	0.0
DS01	0.216	0.0
DS02	-0.314	0.0
DS04	-0.17	0.0
DS0c	-0.113	0.0
GP01	-0.461	0.0
GP02	0.274	0.0
GP0c	-0.714	0.0
NOD	0.57	0.0
NZO	0.088	0.0
PWK	0.149	0.0
H37Rv_KO_CtpC	-1.037	0.0
H37Rv_KO_CtpD	-0.32	0.127
H37Rv_KO_Rv1272	0.114	0.0
H37Rv_KO_SugABC	0.6	0.0
H37Rv_KO_MbtN	-0.759	0.0
Trans05	0.514	0.0
macrophage_unactivated	0.243	-0.436
IL1	0.228	-0.409
Rapamycin	0.236	-0.424
Tcell	0.459	-0.45
GMCSF	0.903	-0.364
IFNab	0.481	0.729
IFNg	0.786	0.644
IFNg_GMCSF1	0.415	-0.434
Rv1432_day32	-0.106	0.0
Rv1565c_day32	-0.491	-0.766
secA2_input	0.116	-0.216
delta_Rv3594	-0.312	-0.369
delta_Rv3717	0.12	0.955
delta_Rv3811	0.122	0.697
delta_Rv0954	0.018	-0.149
PonA1	0.103	-0.278
EccD1_KO	-0.72	-3.667
EspI_KO	-1.201	-2.264
PE35_KO	-1.873	-2.917
PPE68_KO	-1.565	-1.213
glycerol2	-0.153	0.0
lignocerate	0.346	0.0
oleate	-1.452	0.0
phosphatidylcholine	1.043	0.0
acetate	0.337	0.0
glucAc	0.908	0.0
Rv0950ko	0.112	0.0
Rv1096ko	0.253	0.0
Rv3684ko	0.102	1.14
delta_otsA_trehalose	-0.253	0.0