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 Rv1836c/-

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

	Rv2445c/ndkA	Rv1836c/-
Fe_supp_jason_reseq	4.9	3.703
low_pH_jason_reseq	0.0	-0.44
NO_jason_reseq	0.0	-0.69
B6_jason_reseq	0.0	-0.292
MHCII_jason_reseq	0.0	0.492
Isoniazid02	0.0	-2.187
Rifampicin4	0.0	-2.943
Ethambutol3	0.0	-1.216
Meropenem3	0.0	-1.533
Vancomycin16	0.0	-2.653
Rv2680_day32	0.0	1.226
H37Rv_KO_MarP	-0.26	-6.0
hypoxia_3wks	0.0	-0.961
hypoxia_6wks	0.0	-0.503
glycerol	0.0	-0.202
cholesterol	0.0	0.253
AJ	0.0	-0.232
Bibs02	0.0	-0.183
Bibs02c	0.0	-0.209
BL6	0.0	1.02
BL6a	0.0	1.339
BXD01	0.0	1.272
BXD010	0.0	0.323
BXD011	0.0	1.988
BXD03	0.0	0.341
BXD04	0.0	0.563
BXD05	0.0	1.21
BXD06	0.0	0.523
BXD07	0.0	0.865
BXD08	0.0	1.248
BXD09	0.0	0.95
CAST	0.0	0.21
CCcont	0.0	2.888
DS01	0.0	-0.236
DS02	0.0	-0.217
DS04	0.0	0.883
DS0c	0.0	0.0
GP01	0.0	0.964
GP02	0.0	1.165
GP0c	0.0	1.002
NOD	0.0	-0.225
NZO	0.0	-0.199
PWK	0.0	-0.196
H37Rv_KO_CtpC	0.0	0.739
H37Rv_KO_CtpD	0.0	0.918
H37Rv_KO_Rv1272	0.0	0.953
H37Rv_KO_SugABC	0.0	1.362
H37Rv_KO_MbtN	0.0	1.116
Trans05	0.0	1.066
macrophage_unactivated	0.0	0.669
IL1	0.0	0.0
Rapamycin	0.0	0.227
Tcell	0.0	0.0
GMCSF	0.0	0.38
IFNab	0.0	1.844
IFNg	0.0	1.058
IFNg_GMCSF1	0.0	0.452
Rv1432_day32	0.0	1.748
Rv1565c_day32	0.0	0.0
secA2_input	-2.696	-2.174
delta_Rv3594	1.086	2.695
delta_Rv3717	2.202	3.555
delta_Rv3811	0.187	2.842
delta_Rv0954	0.0	-1.461
PonA1	-0.159	-1.387
EccD1_KO	-1.595	0.148
EspI_KO	0.0	-0.051
PE35_KO	-0.312	-1.496
PPE68_KO	0.896	0.0
glycerol2	0.0	-0.193
lignocerate	0.0	-0.168
oleate	0.0	-0.196
phosphatidylcholine	0.0	-0.193
acetate	0.0	0.0
glucAc	0.0	-0.143
Rv0950ko	-0.416	-6.0
Rv1096ko	2.376	-0.03
Rv3684ko	3.056	1.677
delta_otsA_trehalose	0.0	-0.288