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 Rv3425/PPE57:

update plot	correlation	link to info on gene
Rv3487c/lipF	(cc=0.5702)	info on Rv3487c/lipF
Rv2789c/fadE21	(cc=0.5656)	info on Rv2789c/fadE21
Rv3796/-	(cc=0.5493)	info on Rv3796/-
Rv1918c/PPE35	(cc=0.5469)	info on Rv1918c/PPE35
Rv2430c/PPE41	(cc=0.5459)	info on Rv2430c/PPE41
Rv1500/-	(cc=0.5353)	info on Rv1500/-
Rv2584c/apt	(cc=0.5224)	info on Rv2584c/apt
Rv0469/umaA	(cc=0.522)	info on Rv0469/umaA
Rv0868c/moaD2	(cc=0.5219)	info on Rv0868c/moaD2
Rv0354c/PPE7	(cc=0.518)	info on Rv0354c/PPE7

Correlation of Rv3425/PPE57 with Rv0354c/PPE7

Normalized LFCs for Rv3425/PPE57:
(description and provenance of datasets)

	Rv3425/PPE57	Rv0354c/PPE7
Fe_supp_jason_reseq	0.598	0.131
low_pH_jason_reseq	-0.669	-1.047
NO_jason_reseq	-0.488	-0.26
B6_jason_reseq	-0.79	-1.113
MHCII_jason_reseq	-0.124	-1.462
Isoniazid02	-0.224	-1.225
Rifampicin4	0.206	0.181
Ethambutol3	0.092	-0.63
Meropenem3	-0.096	-0.53
Vancomycin16	0.05	-0.406
Rv2680_day32	-0.384	0.453
H37Rv_KO_MarP	1.099	-0.322
hypoxia_3wks	0.215	-0.455
hypoxia_6wks	0.451	-0.593
glycerol	0.404	0.809
cholesterol	-0.369	0.709
AJ	0.429	0.746
Bibs02	-0.775	0.278
Bibs02c	0.856	0.799
BL6	0.421	1.261
BL6a	1.065	1.124
BXD01	0.637	0.426
BXD010	0.822	1.7
BXD011	0.4	0.983
BXD03	0.746	0.504
BXD04	0.642	0.365
BXD05	1.02	0.909
BXD06	0.444	0.539
BXD07	0.916	0.567
BXD08	0.604	0.844
BXD09	0.845	0.76
CAST	0.389	0.506
CCcont	0.365	0.885
DS01	0.623	0.376
DS02	0.013	0.255
DS04	-0.16	-0.247
DS0c	0.366	-0.306
GP01	0.413	1.33
GP02	0.959	0.727
GP0c	0.689	0.471
NOD	0.146	0.182
NZO	1.144	1.208
PWK	-0.269	-0.242
H37Rv_KO_CtpC	0.59	1.43
H37Rv_KO_CtpD	0.139	1.569
H37Rv_KO_Rv1272	0.317	1.383
H37Rv_KO_SugABC	0.247	-0.546
H37Rv_KO_MbtN	0.396	0.749
Trans05	0.463	1.526
macrophage_unactivated	0.502	0.704
IL1	0.122	0.217
Rapamycin	0.19	0.117
Tcell	0.499	0.388
GMCSF	-0.288	-0.222
IFNab	0.042	-0.369
IFNg	0.791	0.238
IFNg_GMCSF1	0.949	0.261
Rv1432_day32	0.233	0.278
Rv1565c_day32	-0.531	-1.978
secA2_input	-0.454	0.31
delta_Rv3594	-0.069	-0.011
delta_Rv3717	-1.0	0.052
delta_Rv3811	0.033	0.281
delta_Rv0954	0.181	0.439
PonA1	0.208	-0.403
EccD1_KO	-0.743	-0.71
EspI_KO	-0.607	-0.362
PE35_KO	-1.199	-0.292
PPE68_KO	-0.602	-0.474
glycerol2	0.395	0.701
lignocerate	0.619	1.011
oleate	0.624	0.384
phosphatidylcholine	0.829	0.727
acetate	0.078	-0.057
glucAc	0.095	0.545
Rv0950ko	-0.208	1.07
Rv1096ko	-1.161	0.353
Rv3684ko	-0.737	0.439
delta_otsA_trehalose	-0.32	-0.642