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 Rv2164c/-:

update plot	correlation	link to info on gene
Rv2678c/hemE	(cc=0.761)	info on Rv2678c/hemE
Rv3858c/gltD	(cc=0.6997)	info on Rv3858c/gltD
Rv0541c/-	(cc=0.6988)	info on Rv0541c/-
Rv3918c/parA	(cc=0.6919)	info on Rv3918c/parA
Rv0701/rplC	(cc=0.6902)	info on Rv0701/rplC
Rv2697c/dut	(cc=0.6849)	info on Rv2697c/dut
Rv3764c/tcrY	(cc=0.6649)	info on Rv3764c/tcrY
Rv3456c/rplQ	(cc=0.6568)	info on Rv3456c/rplQ
Rv3673c/-	(cc=0.6566)	info on Rv3673c/-
Rv2611c/-	(cc=0.637)	info on Rv2611c/-

Correlation of Rv2164c/- with Rv3858c/gltD

Normalized LFCs for Rv2164c/-:
(description and provenance of datasets)

	Rv2164c/-	Rv3858c/gltD
Fe_supp_jason_reseq	0.0	0.0
low_pH_jason_reseq	0.0	0.44
NO_jason_reseq	0.0	0.0
B6_jason_reseq	0.0	0.0
MHCII_jason_reseq	0.0	0.0
Isoniazid02	0.0	0.0
Rifampicin4	0.0	0.0
Ethambutol3	0.0	0.0
Meropenem3	0.0	0.0
Vancomycin16	0.0	0.0
Rv2680_day32	0.0	0.0
H37Rv_KO_MarP	0.0	0.0
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	0.0	0.0
DS01	0.0	0.0
DS02	0.0	0.0
DS04	0.0	0.0
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	0.0
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	0.0	-1.45
delta_Rv3594	1.416	0.0
delta_Rv3717	1.803	0.0
delta_Rv3811	1.487	0.0
delta_Rv0954	0.0	0.178
PonA1	1.313	0.0
EccD1_KO	-0.22	-2.592
EspI_KO	-2.852	-2.247
PE35_KO	-2.917	-1.934
PPE68_KO	-2.796	-2.963
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	-0.669
Rv1096ko	-0.416	-1.463
Rv3684ko	-0.452	-0.35
delta_otsA_trehalose	0.0	0.0