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 Rv3487c/lipF

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

	Rv3425/PPE57	Rv3487c/lipF
Fe_supp_jason_reseq	0.598	-0.019
low_pH_jason_reseq	-0.669	-1.251
NO_jason_reseq	-0.488	-0.239
B6_jason_reseq	-0.79	-0.625
MHCII_jason_reseq	-0.124	-0.39
Isoniazid02	-0.224	0.253
Rifampicin4	0.206	0.084
Ethambutol3	0.092	0.445
Meropenem3	-0.096	-0.216
Vancomycin16	0.05	-0.151
Rv2680_day32	-0.384	-0.366
H37Rv_KO_MarP	1.099	0.374
hypoxia_3wks	0.215	0.072
hypoxia_6wks	0.451	0.58
glycerol	0.404	-0.127
cholesterol	-0.369	-0.321
AJ	0.429	0.242
Bibs02	-0.775	0.181
Bibs02c	0.856	-0.299
BL6	0.421	0.189
BL6a	1.065	0.083
BXD01	0.637	0.158
BXD010	0.822	0.391
BXD011	0.4	0.364
BXD03	0.746	0.223
BXD04	0.642	0.761
BXD05	1.02	0.801
BXD06	0.444	0.025
BXD07	0.916	0.311
BXD08	0.604	0.615
BXD09	0.845	0.034
CAST	0.389	0.457
CCcont	0.365	0.187
DS01	0.623	0.031
DS02	0.013	-0.447
DS04	-0.16	0.777
DS0c	0.366	-0.676
GP01	0.413	0.17
GP02	0.959	1.009
GP0c	0.689	-0.039
NOD	0.146	0.703
NZO	1.144	-0.143
PWK	-0.269	0.595
H37Rv_KO_CtpC	0.59	0.674
H37Rv_KO_CtpD	0.139	0.353
H37Rv_KO_Rv1272	0.317	0.153
H37Rv_KO_SugABC	0.247	0.648
H37Rv_KO_MbtN	0.396	0.375
Trans05	0.463	0.556
macrophage_unactivated	0.502	0.256
IL1	0.122	-0.059
Rapamycin	0.19	-0.031
Tcell	0.499	0.042
GMCSF	-0.288	-0.209
IFNab	0.042	-0.082
IFNg	0.791	0.462
IFNg_GMCSF1	0.949	0.163
Rv1432_day32	0.233	0.808
Rv1565c_day32	-0.531	0.419
secA2_input	-0.454	0.122
delta_Rv3594	-0.069	-0.378
delta_Rv3717	-1.0	-0.602
delta_Rv3811	0.033	-0.47
delta_Rv0954	0.181	-0.77
PonA1	0.208	-0.34
EccD1_KO	-0.743	-0.118
EspI_KO	-0.607	-0.262
PE35_KO	-1.199	-1.105
PPE68_KO	-0.602	-0.752
glycerol2	0.395	0.604
lignocerate	0.619	0.57
oleate	0.624	0.693
phosphatidylcholine	0.829	0.787
acetate	0.078	-0.274
glucAc	0.095	0.247
Rv0950ko	-0.208	0.374
Rv1096ko	-1.161	-0.543
Rv3684ko	-0.737	-1.123
delta_otsA_trehalose	-0.32	-0.799