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 Rv0220/lipC:

update plot	correlation	link to info on gene
Rv0822c/-	(cc=0.6166)	info on Rv0822c/-
Rv3675/-	(cc=0.5392)	info on Rv3675/-
Rv0222/echA1	(cc=0.534)	info on Rv0222/echA1
Rv3840/-	(cc=0.532)	info on Rv3840/-
Rv1517/-	(cc=0.5306)	info on Rv1517/-
Rv2443/dctA	(cc=0.5285)	info on Rv2443/dctA
Rv2584c/apt	(cc=0.5261)	info on Rv2584c/apt
Rv1720c/vapC12	(cc=0.522)	info on Rv1720c/vapC12
Rv2430c/PPE41	(cc=0.5191)	info on Rv2430c/PPE41
Rv3847/-	(cc=0.5191)	info on Rv3847/-

Correlation of Rv0220/lipC with Rv1517/-

Normalized LFCs for Rv0220/lipC:
(description and provenance of datasets)

	Rv0220/lipC	Rv1517/-
Fe_supp_jason_reseq	-0.172	0.3
low_pH_jason_reseq	-0.564	0.207
NO_jason_reseq	-0.551	-0.465
B6_jason_reseq	-0.6	0.119
MHCII_jason_reseq	-0.075	-1.348
Isoniazid02	0.143	0.323
Rifampicin4	-0.596	-0.065
Ethambutol3	0.452	-0.32
Meropenem3	0.041	-0.151
Vancomycin16	-0.329	0.422
Rv2680_day32	-0.125	1.165
H37Rv_KO_MarP	0.301	0.406
hypoxia_3wks	0.195	0.0
hypoxia_6wks	-0.106	-0.624
glycerol	0.65	0.13
cholesterol	0.142	-0.261
AJ	0.155	0.22
Bibs02	1.02	0.03
Bibs02c	-0.815	-1.105
BL6	0.304	0.437
BL6a	-0.069	0.872
BXD01	0.022	0.629
BXD010	0.506	1.321
BXD011	0.472	1.054
BXD03	1.002	1.721
BXD04	0.896	0.811
BXD05	1.107	0.784
BXD06	0.131	1.457
BXD07	0.579	0.793
BXD08	0.445	1.007
BXD09	0.435	1.458
CAST	0.592	0.287
CCcont	-0.279	-0.3
DS01	0.51	-0.38
DS02	0.247	-0.715
DS04	0.419	0.155
DS0c	0.179	-1.087
GP01	1.623	0.497
GP02	1.416	1.357
GP0c	0.602	1.188
NOD	0.454	1.014
NZO	-0.254	-1.225
PWK	0.311	0.216
H37Rv_KO_CtpC	-0.086	1.164
H37Rv_KO_CtpD	0.939	1.397
H37Rv_KO_Rv1272	0.683	1.365
H37Rv_KO_SugABC	0.814	1.696
H37Rv_KO_MbtN	-0.376	-0.799
Trans05	-0.576	0.425
macrophage_unactivated	0.922	1.212
IL1	0.142	1.163
Rapamycin	-0.203	1.255
Tcell	-0.052	0.388
GMCSF	0.842	0.655
IFNab	0.638	0.75
IFNg	0.331	1.139
IFNg_GMCSF1	0.663	0.534
Rv1432_day32	0.0	0.0
Rv1565c_day32	-0.823	-0.254
secA2_input	-0.817	0.294
delta_Rv3594	-0.242	-0.733
delta_Rv3717	-0.307	-0.496
delta_Rv3811	-0.299	-0.247
delta_Rv0954	0.227	-0.509
PonA1	0.084	0.22
EccD1_KO	-0.628	0.26
EspI_KO	-0.642	-0.596
PE35_KO	-0.362	0.14
PPE68_KO	-0.889	-0.378
glycerol2	0.021	-0.353
lignocerate	-0.357	-0.546
oleate	0.142	-0.197
phosphatidylcholine	-0.172	1.137
acetate	-0.427	-0.53
glucAc	-0.523	-0.56
Rv0950ko	-0.314	0.048
Rv1096ko	0.235	0.784
Rv3684ko	-0.94	-0.377
delta_otsA_trehalose	0.317	0.214