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 Rv3606c/folK

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

	Rv2445c/ndkA	Rv3606c/folK
Fe_supp_jason_reseq	4.9	1.204
low_pH_jason_reseq	0.0	-0.151
NO_jason_reseq	0.0	-1.205
B6_jason_reseq	0.0	1.552
MHCII_jason_reseq	0.0	1.843
Isoniazid02	0.0	-0.162
Rifampicin4	0.0	0.785
Ethambutol3	0.0	0.455
Meropenem3	0.0	-0.204
Vancomycin16	0.0	0.528
Rv2680_day32	0.0	-0.684
H37Rv_KO_MarP	-0.26	-0.936
hypoxia_3wks	0.0	-1.467
hypoxia_6wks	0.0	-0.768
glycerol	0.0	-0.923
cholesterol	0.0	-0.238
AJ	0.0	1.656
Bibs02	0.0	0.637
Bibs02c	0.0	-0.141
BL6	0.0	-0.114
BL6a	0.0	0.462
BXD01	0.0	0.348
BXD010	0.0	-1.856
BXD011	0.0	0.106
BXD03	0.0	-2.083
BXD04	0.0	-1.42
BXD05	0.0	-0.709
BXD06	0.0	-1.026
BXD07	0.0	-0.68
BXD08	0.0	-1.288
BXD09	0.0	-0.464
CAST	0.0	0.839
CCcont	0.0	-0.842
DS01	0.0	1.786
DS02	0.0	0.181
DS04	0.0	2.097
DS0c	0.0	0.79
GP01	0.0	-1.012
GP02	0.0	-1.364
GP0c	0.0	-0.942
NOD	0.0	0.485
NZO	0.0	1.822
PWK	0.0	0.887
H37Rv_KO_CtpC	0.0	-0.856
H37Rv_KO_CtpD	0.0	-1.835
H37Rv_KO_Rv1272	0.0	-1.29
H37Rv_KO_SugABC	0.0	-1.204
H37Rv_KO_MbtN	0.0	-0.437
Trans05	0.0	0.305
macrophage_unactivated	0.0	-0.193
IL1	0.0	-1.231
Rapamycin	0.0	-1.034
Tcell	0.0	0.192
GMCSF	0.0	-1.096
IFNab	0.0	-1.769
IFNg	0.0	-1.109
IFNg_GMCSF1	0.0	-1.562
Rv1432_day32	0.0	-0.961
Rv1565c_day32	0.0	0.0
secA2_input	-2.696	-3.428
delta_Rv3594	1.086	0.522
delta_Rv3717	2.202	-0.083
delta_Rv3811	0.187	0.79
delta_Rv0954	0.0	-0.578
PonA1	-0.159	-0.675
EccD1_KO	-1.595	-1.783
EspI_KO	0.0	-2.518
PE35_KO	-0.312	-1.808
PPE68_KO	0.896	-2.339
glycerol2	0.0	0.597
lignocerate	0.0	0.054
oleate	0.0	0.183
phosphatidylcholine	0.0	0.062
acetate	0.0	0.214
glucAc	0.0	0.176
Rv0950ko	-0.416	0.241
Rv1096ko	2.376	1.638
Rv3684ko	3.056	2.777
delta_otsA_trehalose	0.0	-1.645