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 Rv3621c/PPE65:

update plot	correlation	link to info on gene
Rv1894c/-	(cc=0.4567)	info on Rv1894c/-
Rv3055/-	(cc=0.423)	info on Rv3055/-
Rv0577/TB27.3	(cc=0.4204)	info on Rv0577/TB27.3
Rv2079/-	(cc=0.4061)	info on Rv2079/-
Rv2025c/-	(cc=0.4017)	info on Rv2025c/-
Rv0962c/lprP	(cc=0.387)	info on Rv0962c/lprP
Rv1053c/-	(cc=0.3814)	info on Rv1053c/-
Rv1760/-	(cc=0.381)	info on Rv1760/-
Rv3595c/PE_PGRS59	(cc=0.3806)	info on Rv3595c/PE_PGRS59
Rv2755c/hsdS.1	(cc=0.3681)	info on Rv2755c/hsdS.1

Correlation of Rv3621c/PPE65 with Rv1760/-

Normalized LFCs for Rv3621c/PPE65:
(description and provenance of datasets)

	Rv3621c/PPE65	Rv1760/-
Fe_supp_jason_reseq	1.108	0.36
low_pH_jason_reseq	-0.261	-1.173
NO_jason_reseq	-0.139	0.333
B6_jason_reseq	0.629	0.16
MHCII_jason_reseq	0.742	0.248
Isoniazid02	-0.019	0.278
Rifampicin4	-0.141	0.016
Ethambutol3	0.0	0.28
Meropenem3	1.579	1.035
Vancomycin16	0.199	0.119
Rv2680_day32	0.526	-0.408
H37Rv_KO_MarP	0.044	-0.141
hypoxia_3wks	0.024	-0.064
hypoxia_6wks	-0.173	0.098
glycerol	0.221	0.176
cholesterol	-0.431	0.434
AJ	0.405	0.745
Bibs02	0.261	0.065
Bibs02c	-0.246	-0.07
BL6	0.188	0.0
BL6a	-0.172	-0.195
BXD01	0.18	0.028
BXD010	-0.825	-0.168
BXD011	1.466	0.041
BXD03	0.262	-0.245
BXD04	0.245	0.044
BXD05	-0.237	-0.117
BXD06	-0.102	-0.196
BXD07	0.263	-0.306
BXD08	0.475	0.298
BXD09	0.188	-0.189
CAST	0.252	0.405
CCcont	0.301	-0.106
DS01	-0.145	0.252
DS02	-0.233	0.153
DS04	0.628	-0.056
DS0c	-0.189	0.159
GP01	-0.032	0.953
GP02	1.109	1.058
GP0c	0.366	0.478
NOD	0.918	0.849
NZO	0.965	0.63
PWK	0.601	0.529
H37Rv_KO_CtpC	0.289	0.162
H37Rv_KO_CtpD	-0.041	0.262
H37Rv_KO_Rv1272	0.403	0.751
H37Rv_KO_SugABC	0.426	-0.21
H37Rv_KO_MbtN	0.723	0.494
Trans05	1.268	0.36
macrophage_unactivated	0.312	0.271
IL1	-0.697	-0.347
Rapamycin	0.018	-0.457
Tcell	0.062	-0.339
GMCSF	0.306	-0.032
IFNab	0.227	-0.472
IFNg	-0.158	0.0
IFNg_GMCSF1	0.808	0.83
Rv1432_day32	-0.546	0.082
Rv1565c_day32	0.483	-0.125
secA2_input	0.282	-0.18
delta_Rv3594	-0.179	-0.067
delta_Rv3717	-0.483	0.006
delta_Rv3811	-0.103	0.071
delta_Rv0954	-0.224	0.317
PonA1	0.328	0.15
EccD1_KO	0.875	-0.622
EspI_KO	0.086	-0.716
PE35_KO	0.557	-0.365
PPE68_KO	0.467	-0.301
glycerol2	0.667	0.391
lignocerate	0.665	0.592
oleate	0.469	0.285
phosphatidylcholine	0.577	0.609
acetate	0.168	-0.101
glucAc	0.121	0.213
Rv0950ko	0.956	0.467
Rv1096ko	0.642	-0.106
Rv3684ko	0.717	0.151
delta_otsA_trehalose	-0.261	0.432