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 Rv2946c/pks1

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

	Rv3698/-	Rv2946c/pks1
Fe_supp_jason_reseq	0.286	0.14
low_pH_jason_reseq	-0.489	-0.903
NO_jason_reseq	-1.173	-0.987
B6_jason_reseq	-0.324	-0.23
MHCII_jason_reseq	1.101	-0.172
Isoniazid02	-0.16	-0.068
Rifampicin4	-0.298	-0.171
Ethambutol3	1.987	0.705
Meropenem3	1.198	0.303
Vancomycin16	0.111	-0.082
Rv2680_day32	0.204	-1.387
H37Rv_KO_MarP	0.871	-0.703
hypoxia_3wks	0.383	1.168
hypoxia_6wks	0.0	1.247
glycerol	0.312	0.455
cholesterol	0.146	0.541
AJ	-0.183	-0.968
Bibs02	-0.085	0.162
Bibs02c	0.323	0.135
BL6	0.303	-0.149
BL6a	0.55	0.039
BXD01	0.924	0.222
BXD010	0.496	-0.079
BXD011	0.508	0.074
BXD03	0.989	0.253
BXD04	1.336	0.486
BXD05	0.766	-0.083
BXD06	0.37	0.009
BXD07	0.384	0.036
BXD08	1.061	0.473
BXD09	0.272	-0.047
CAST	-0.502	-1.078
CCcont	1.024	0.329
DS01	0.334	0.015
DS02	0.096	-0.358
DS04	0.299	0.298
DS0c	1.365	-0.291
GP01	0.297	0.518
GP02	0.764	-0.051
GP0c	0.491	0.399
NOD	-0.329	-1.245
NZO	-0.672	-1.039
PWK	0.252	-0.838
H37Rv_KO_CtpC	-0.325	-0.181
H37Rv_KO_CtpD	0.366	0.05
H37Rv_KO_Rv1272	0.375	-0.418
H37Rv_KO_SugABC	0.374	0.841
H37Rv_KO_MbtN	0.132	0.494
Trans05	0.408	-0.155
macrophage_unactivated	2.149	0.259
IL1	-0.059	0.43
Rapamycin	0.976	0.528
Tcell	1.189	0.694
GMCSF	0.053	0.177
IFNab	1.103	0.877
IFNg	0.722	-0.061
IFNg_GMCSF1	0.528	-0.025
Rv1432_day32	0.021	-0.947
Rv1565c_day32	-0.283	-0.253
secA2_input	-0.163	-0.39
delta_Rv3594	0.967	0.639
delta_Rv3717	-0.191	0.094
delta_Rv3811	-0.138	0.634
delta_Rv0954	1.083	0.592
PonA1	-0.043	0.248
EccD1_KO	0.405	-0.214
EspI_KO	0.516	0.325
PE35_KO	0.461	-0.053
PPE68_KO	0.653	-0.029
glycerol2	0.042	0.0
lignocerate	0.239	-0.195
oleate	0.333	0.121
phosphatidylcholine	0.434	0.041
acetate	0.326	-0.564
glucAc	0.381	-0.461
Rv0950ko	0.262	0.181
Rv1096ko	-0.139	0.027
Rv3684ko	-0.717	-0.354
delta_otsA_trehalose	-0.439	-0.527