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 Rv2789c/fadE21

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

	Rv3425/PPE57	Rv2789c/fadE21
Fe_supp_jason_reseq	0.598	0.182
low_pH_jason_reseq	-0.669	-1.134
NO_jason_reseq	-0.488	-0.788
B6_jason_reseq	-0.79	-0.752
MHCII_jason_reseq	-0.124	-0.446
Isoniazid02	-0.224	-0.096
Rifampicin4	0.206	0.087
Ethambutol3	0.092	0.32
Meropenem3	-0.096	0.662
Vancomycin16	0.05	0.626
Rv2680_day32	-0.384	-0.554
H37Rv_KO_MarP	1.099	0.858
hypoxia_3wks	0.215	-0.116
hypoxia_6wks	0.451	-0.123
glycerol	0.404	-0.335
cholesterol	-0.369	0.208
AJ	0.429	-0.072
Bibs02	-0.775	-0.115
Bibs02c	0.856	2.292
BL6	0.421	1.213
BL6a	1.065	1.992
BXD01	0.637	1.215
BXD010	0.822	0.967
BXD011	0.4	1.017
BXD03	0.746	1.099
BXD04	0.642	0.073
BXD05	1.02	0.726
BXD06	0.444	0.645
BXD07	0.916	0.846
BXD08	0.604	1.224
BXD09	0.845	1.018
CAST	0.389	-0.382
CCcont	0.365	1.832
DS01	0.623	1.562
DS02	0.013	1.134
DS04	-0.16	0.059
DS0c	0.366	2.641
GP01	0.413	2.281
GP02	0.959	1.632
GP0c	0.689	1.322
NOD	0.146	2.556
NZO	1.144	-1.107
PWK	-0.269	0.332
H37Rv_KO_CtpC	0.59	1.93
H37Rv_KO_CtpD	0.139	1.332
H37Rv_KO_Rv1272	0.317	0.084
H37Rv_KO_SugABC	0.247	-1.168
H37Rv_KO_MbtN	0.396	0.253
Trans05	0.463	0.554
macrophage_unactivated	0.502	1.509
IL1	0.122	0.297
Rapamycin	0.19	1.114
Tcell	0.499	0.401
GMCSF	-0.288	-0.069
IFNab	0.042	0.514
IFNg	0.791	0.748
IFNg_GMCSF1	0.949	0.534
Rv1432_day32	0.233	0.668
Rv1565c_day32	-0.531	0.231
secA2_input	-0.454	-0.571
delta_Rv3594	-0.069	-0.167
delta_Rv3717	-1.0	-0.347
delta_Rv3811	0.033	-0.195
delta_Rv0954	0.181	-0.027
PonA1	0.208	-0.471
EccD1_KO	-0.743	-1.0
EspI_KO	-0.607	-1.064
PE35_KO	-1.199	-0.755
PPE68_KO	-0.602	-1.046
glycerol2	0.395	1.379
lignocerate	0.619	1.61
oleate	0.624	0.342
phosphatidylcholine	0.829	1.49
acetate	0.078	0.973
glucAc	0.095	1.254
Rv0950ko	-0.208	0.712
Rv1096ko	-1.161	-0.443
Rv3684ko	-0.737	0.295
delta_otsA_trehalose	-0.32	-0.965