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 Rv1225c/-

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

	Rv3698/-	Rv1225c/-
Fe_supp_jason_reseq	0.286	0.166
low_pH_jason_reseq	-0.489	-1.839
NO_jason_reseq	-1.173	-0.971
B6_jason_reseq	-0.324	-0.652
MHCII_jason_reseq	1.101	-0.388
Isoniazid02	-0.16	1.232
Rifampicin4	-0.298	-0.233
Ethambutol3	1.987	1.828
Meropenem3	1.198	0.134
Vancomycin16	0.111	0.034
Rv2680_day32	0.204	-1.898
H37Rv_KO_MarP	0.871	0.962
hypoxia_3wks	0.383	0.02
hypoxia_6wks	0.0	-0.305
glycerol	0.312	-0.269
cholesterol	0.146	0.101
AJ	-0.183	0.941
Bibs02	-0.085	-0.017
Bibs02c	0.323	0.403
BL6	0.303	1.054
BL6a	0.55	1.224
BXD01	0.924	0.494
BXD010	0.496	0.273
BXD011	0.508	0.521
BXD03	0.989	1.28
BXD04	1.336	1.625
BXD05	0.766	1.146
BXD06	0.37	0.351
BXD07	0.384	0.199
BXD08	1.061	0.715
BXD09	0.272	0.62
CAST	-0.502	-0.988
CCcont	1.024	0.794
DS01	0.334	0.067
DS02	0.096	-0.243
DS04	0.299	-0.977
DS0c	1.365	-0.255
GP01	0.297	0.182
GP02	0.764	1.224
GP0c	0.491	-0.038
NOD	-0.329	-0.426
NZO	-0.672	0.201
PWK	0.252	-0.703
H37Rv_KO_CtpC	-0.325	1.589
H37Rv_KO_CtpD	0.366	0.717
H37Rv_KO_Rv1272	0.375	0.272
H37Rv_KO_SugABC	0.374	0.356
H37Rv_KO_MbtN	0.132	-0.025
Trans05	0.408	-0.425
macrophage_unactivated	2.149	0.085
IL1	-0.059	1.317
Rapamycin	0.976	1.102
Tcell	1.189	0.485
GMCSF	0.053	0.61
IFNab	1.103	0.901
IFNg	0.722	0.388
IFNg_GMCSF1	0.528	0.22
Rv1432_day32	0.021	0.859
Rv1565c_day32	-0.283	-0.469
secA2_input	-0.163	-0.294
delta_Rv3594	0.967	0.315
delta_Rv3717	-0.191	0.043
delta_Rv3811	-0.138	0.333
delta_Rv0954	1.083	0.625
PonA1	-0.043	0.899
EccD1_KO	0.405	1.299
EspI_KO	0.516	1.908
PE35_KO	0.461	1.286
PPE68_KO	0.653	0.902
glycerol2	0.042	0.45
lignocerate	0.239	0.509
oleate	0.333	0.42
phosphatidylcholine	0.434	0.681
acetate	0.326	0.263
glucAc	0.381	0.306
Rv0950ko	0.262	-0.389
Rv1096ko	-0.139	-0.645
Rv3684ko	-0.717	-0.829
delta_otsA_trehalose	-0.439	-1.323