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 Rv1406/fmt:

update plot	correlation	link to info on gene
Rv3671c/-	(cc=0.7245)	info on Rv3671c/-
Rv2392/cysH	(cc=0.6574)	info on Rv2392/cysH
Rv3101c/ftsX	(cc=0.5706)	info on Rv3101c/ftsX
Rv2439c/proB	(cc=0.5567)	info on Rv2439c/proB
Rv0811c/-	(cc=0.5484)	info on Rv0811c/-
Rv3258c/-	(cc=0.5471)	info on Rv3258c/-
Rv3789/-	(cc=0.5139)	info on Rv3789/-
Rv2229c/-	(cc=0.4912)	info on Rv2229c/-
Rv3670/ephE	(cc=0.4553)	info on Rv3670/ephE
Rv0736/rslA	(cc=0.4406)	info on Rv0736/rslA

Correlation of Rv1406/fmt with Rv3670/ephE

Normalized LFCs for Rv1406/fmt:
(description and provenance of datasets)

	Rv1406/fmt	Rv3670/ephE
Fe_supp_jason_reseq	0.0	1.209
low_pH_jason_reseq	0.231	0.0
NO_jason_reseq	0.0	0.362
B6_jason_reseq	0.0	0.0
MHCII_jason_reseq	0.0	0.0
Isoniazid02	0.0	0.0
Rifampicin4	0.0	0.0
Ethambutol3	0.0	0.0
Meropenem3	0.0	0.0
Vancomycin16	0.0	0.0
Rv2680_day32	0.0	-1.357
H37Rv_KO_MarP	-1.197	-2.095
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	0.127	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	0.0	0.149
DS01	0.0	0.0
DS02	0.0	0.0
DS04	0.0	0.953
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	0.348
H37Rv_KO_MbtN	0.0	0.283
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	0.216	-0.216
delta_Rv3594	0.315	0.266
delta_Rv3717	-0.477	1.669
delta_Rv3811	0.446	0.126
delta_Rv0954	-0.149	-4.534
PonA1	-0.437	-0.866
EccD1_KO	-0.378	-2.355
EspI_KO	-0.687	-4.894
PE35_KO	-0.335	-3.949
PPE68_KO	0.0	-3.404
glycerol2	0.0	0.0
lignocerate	0.0	0.0
oleate	0.0	0.0
phosphatidylcholine	0.0	0.0
acetate	0.0	0.0
glucAc	0.0	0.0
Rv0950ko	-0.416	1.049
Rv1096ko	1.632	0.727
Rv3684ko	1.464	2.325
delta_otsA_trehalose	0.0	-1.743