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 Rv3698/-:

update plot	correlation	link to info on gene
Rv2946c/pks1	(cc=0.4727)	info on Rv2946c/pks1
Rv1879/-	(cc=0.4573)	info on Rv1879/-
Rv1225c/-	(cc=0.4465)	info on Rv1225c/-
Rv2887/-	(cc=0.4386)	info on Rv2887/-
Rv0328/-	(cc=0.4369)	info on Rv0328/-
Rv1665/pks11	(cc=0.4259)	info on Rv1665/pks11
Rv2218/lipA	(cc=0.418)	info on Rv2218/lipA
Rv1831/-	(cc=0.4171)	info on Rv1831/-
Rv1748/-	(cc=0.4107)	info on Rv1748/-
Rv1398c/vapB10	(cc=0.4008)	info on Rv1398c/vapB10

Correlation of Rv3698/- with Rv1398c/vapB10

Normalized LFCs for Rv3698/-:
(description and provenance of datasets)

	Rv3698/-	Rv1398c/vapB10
Fe_supp_jason_reseq	0.286	-0.834
low_pH_jason_reseq	-0.489	-0.773
NO_jason_reseq	-1.173	-0.189
B6_jason_reseq	-0.324	-1.519
MHCII_jason_reseq	1.101	0.368
Isoniazid02	-0.16	0.976
Rifampicin4	-0.298	-1.018
Ethambutol3	1.987	1.727
Meropenem3	1.198	-0.223
Vancomycin16	0.111	-0.305
Rv2680_day32	0.204	-0.968
H37Rv_KO_MarP	0.871	-0.59
hypoxia_3wks	0.383	0.622
hypoxia_6wks	0.0	-1.006
glycerol	0.312	1.81
cholesterol	0.146	0.282
AJ	-0.183	-0.373
Bibs02	-0.085	0.083
Bibs02c	0.323	0.638
BL6	0.303	1.081
BL6a	0.55	0.763
BXD01	0.924	0.968
BXD010	0.496	0.777
BXD011	0.508	-0.125
BXD03	0.989	0.847
BXD04	1.336	0.663
BXD05	0.766	-0.159
BXD06	0.37	0.061
BXD07	0.384	0.93
BXD08	1.061	1.599
BXD09	0.272	0.359
CAST	-0.502	0.085
CCcont	1.024	0.833
DS01	0.334	1.266
DS02	0.096	-0.654
DS04	0.299	1.114
DS0c	1.365	1.315
GP01	0.297	-1.062
GP02	0.764	0.618
GP0c	0.491	0.768
NOD	-0.329	2.298
NZO	-0.672	-0.808
PWK	0.252	-0.449
H37Rv_KO_CtpC	-0.325	1.43
H37Rv_KO_CtpD	0.366	1.668
H37Rv_KO_Rv1272	0.375	1.593
H37Rv_KO_SugABC	0.374	-1.297
H37Rv_KO_MbtN	0.132	-1.419
Trans05	0.408	0.529
macrophage_unactivated	2.149	0.799
IL1	-0.059	0.575
Rapamycin	0.976	0.534
Tcell	1.189	2.281
GMCSF	0.053	-0.124
IFNab	1.103	0.556
IFNg	0.722	0.676
IFNg_GMCSF1	0.528	0.179
Rv1432_day32	0.021	0.911
Rv1565c_day32	-0.283	0.199
secA2_input	-0.163	-1.766
delta_Rv3594	0.967	0.734
delta_Rv3717	-0.191	-0.274
delta_Rv3811	-0.138	0.819
delta_Rv0954	1.083	0.017
PonA1	-0.043	-0.375
EccD1_KO	0.405	-0.747
EspI_KO	0.516	-0.191
PE35_KO	0.461	1.219
PPE68_KO	0.653	1.245
glycerol2	0.042	0.287
lignocerate	0.239	0.18
oleate	0.333	0.79
phosphatidylcholine	0.434	0.753
acetate	0.326	-0.166
glucAc	0.381	-0.53
Rv0950ko	0.262	0.084
Rv1096ko	-0.139	0.166
Rv3684ko	-0.717	-1.389
delta_otsA_trehalose	-0.439	0.099