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 Rv2445c/ndkA:

update plot	correlation	link to info on gene
Rv2392/cysH	(cc=0.6185)	info on Rv2392/cysH
Rv0287/esxG	(cc=0.5357)	info on Rv0287/esxG
Rv3208/-	(cc=0.5175)	info on Rv3208/-
Rv2553c/-	(cc=0.4779)	info on Rv2553c/-
Rv3671c/-	(cc=0.4724)	info on Rv3671c/-
Rv3753c/-	(cc=0.4516)	info on Rv3753c/-
Rv2221c/glnE	(cc=0.4248)	info on Rv2221c/glnE
Rv3606c/folK	(cc=0.4226)	info on Rv3606c/folK
Rv1086/-	(cc=0.4207)	info on Rv1086/-
Rv1836c/-	(cc=0.4183)	info on Rv1836c/-

Correlation of Rv2445c/ndkA with Rv3671c/-

Normalized LFCs for Rv2445c/ndkA:
(description and provenance of datasets)

	Rv2445c/ndkA	Rv3671c/-
Fe_supp_jason_reseq	4.9	0.415
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	-0.201
Rifampicin4	0.0	-0.374
Ethambutol3	0.0	-0.168
Meropenem3	0.0	-0.165
Vancomycin16	0.0	-0.366
Rv2680_day32	0.0	0.0
H37Rv_KO_MarP	-0.26	-4.019
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	0.633
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	0.241
H37Rv_KO_Rv1272	0.0	0.0
H37Rv_KO_SugABC	0.0	0.099
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	-2.696	-1.199
delta_Rv3594	1.086	1.672
delta_Rv3717	2.202	0.429
delta_Rv3811	0.187	1.414
delta_Rv0954	0.0	0.627
PonA1	-0.159	-0.516
EccD1_KO	-1.595	-1.417
EspI_KO	0.0	-0.724
PE35_KO	-0.312	-0.137
PPE68_KO	0.896	-0.813
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	-2.044
Rv1096ko	2.376	1.08
Rv3684ko	3.056	2.473
delta_otsA_trehalose	0.0	1.005