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 Rv3035/-:

update plot	correlation	link to info on gene
Rv2256c/-	(cc=0.8624)	info on Rv2256c/-
Rv3044/fecB	(cc=0.8111)	info on Rv3044/fecB
Rv3588c/canB	(cc=0.7468)	info on Rv3588c/canB
Rv2399c/cysT	(cc=0.7417)	info on Rv2399c/cysT
Rv2844/-	(cc=0.729)	info on Rv2844/-
Rv2198c/mmpS3	(cc=0.7275)	info on Rv2198c/mmpS3
Rv3410c/guaB3	(cc=0.7266)	info on Rv3410c/guaB3
Rv2397c/cysA1	(cc=0.7261)	info on Rv2397c/cysA1
Rv2400c/subI	(cc=0.6908)	info on Rv2400c/subI
Rv3902c/-	(cc=0.6788)	info on Rv3902c/-

Correlation of Rv3035/- with Rv2844/-

Normalized LFCs for Rv3035/-:
(description and provenance of datasets)

	Rv3035/-	Rv2844/-
Fe_supp_jason_reseq	0.0	0.0
low_pH_jason_reseq	0.0	0.0
NO_jason_reseq	0.0	0.0
B6_jason_reseq	0.0	0.0
MHCII_jason_reseq	0.0	0.0
Isoniazid02	0.0	-0.383
Rifampicin4	0.0	-0.712
Ethambutol3	0.0	-0.153
Meropenem3	0.0	-0.151
Vancomycin16	0.0	-0.698
Rv2680_day32	0.0	0.0
H37Rv_KO_MarP	-2.167	-3.233
hypoxia_3wks	0.0	0.0
hypoxia_6wks	0.0	0.0
glycerol	0.0	0.0
cholesterol	0.0	0.0
AJ	0.0	0.0
Bibs02	0.0	0.0
Bibs02c	0.0	0.0
BL6	0.0	0.0
BL6a	0.0	0.0
BXD01	0.0	0.0
BXD010	0.0	0.0
BXD011	0.0	0.0
BXD03	0.0	0.0
BXD04	0.0	0.0
BXD05	0.0	0.0
BXD06	0.0	0.0
BXD07	0.0	0.0
BXD08	0.0	0.0
BXD09	0.0	0.0
CAST	0.0	0.0
CCcont	0.149	1.082
DS01	0.0	0.0
DS02	0.0	0.0
DS04	0.0	0.194
DS0c	0.0	0.0
GP01	0.0	0.0
GP02	0.0	0.0
GP0c	0.0	0.0
NOD	0.0	0.0
NZO	0.0	0.0
PWK	0.0	0.0
H37Rv_KO_CtpC	0.0	0.0
H37Rv_KO_CtpD	0.0	0.0
H37Rv_KO_Rv1272	0.0	0.0
H37Rv_KO_SugABC	0.0	0.0
H37Rv_KO_MbtN	0.0	0.103
Trans05	0.0	0.0
macrophage_unactivated	0.0	0.0
IL1	0.0	0.0
Rapamycin	0.0	0.0
Tcell	0.0	0.0
GMCSF	0.0	0.0
IFNab	0.0	0.0
IFNg	0.0	0.0
IFNg_GMCSF1	0.0	0.0
Rv1432_day32	0.0	0.0
Rv1565c_day32	0.0	0.0
secA2_input	0.283	0.388
delta_Rv3594	0.133	0.493
delta_Rv3717	-0.117	-0.331
delta_Rv3811	-0.617	-0.187
delta_Rv0954	0.0	-0.34
PonA1	0.53	1.009
EccD1_KO	-0.865	0.352
EspI_KO	-0.75	-0.687
PE35_KO	1.21	4.728
PPE68_KO	0.0	4.3
glycerol2	0.0	0.0
lignocerate	0.0	0.168
oleate	0.0	0.0
phosphatidylcholine	0.0	0.0
acetate	0.0	0.0
glucAc	0.143	0.0
Rv0950ko	-1.764	-3.015
Rv1096ko	-1.764	-1.873
Rv3684ko	-1.464	-1.359
delta_otsA_trehalose	0.0	0.893