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 Rv2430c/PPE41

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

	Rv3425/PPE57	Rv2430c/PPE41
Fe_supp_jason_reseq	0.598	-0.259
low_pH_jason_reseq	-0.669	-0.617
NO_jason_reseq	-0.488	-0.326
B6_jason_reseq	-0.79	-0.565
MHCII_jason_reseq	-0.124	-1.222
Isoniazid02	-0.224	-0.362
Rifampicin4	0.206	-0.379
Ethambutol3	0.092	-0.539
Meropenem3	-0.096	0.604
Vancomycin16	0.05	-0.541
Rv2680_day32	-0.384	-0.546
H37Rv_KO_MarP	1.099	0.78
hypoxia_3wks	0.215	-0.016
hypoxia_6wks	0.451	-0.558
glycerol	0.404	-1.482
cholesterol	-0.369	-0.355
AJ	0.429	1.329
Bibs02	-0.775	0.293
Bibs02c	0.856	-0.441
BL6	0.421	2.014
BL6a	1.065	1.624
BXD01	0.637	1.73
BXD010	0.822	2.268
BXD011	0.4	2.003
BXD03	0.746	2.085
BXD04	0.642	2.116
BXD05	1.02	2.269
BXD06	0.444	1.836
BXD07	0.916	1.829
BXD08	0.604	1.59
BXD09	0.845	1.891
CAST	0.389	1.024
CCcont	0.365	1.659
DS01	0.623	1.092
DS02	0.013	0.558
DS04	-0.16	0.769
DS0c	0.366	0.509
GP01	0.413	0.134
GP02	0.959	2.462
GP0c	0.689	0.343
NOD	0.146	1.447
NZO	1.144	0.483
PWK	-0.269	0.872
H37Rv_KO_CtpC	0.59	0.914
H37Rv_KO_CtpD	0.139	1.252
H37Rv_KO_Rv1272	0.317	1.399
H37Rv_KO_SugABC	0.247	1.91
H37Rv_KO_MbtN	0.396	1.129
Trans05	0.463	2.226
macrophage_unactivated	0.502	1.076
IL1	0.122	0.125
Rapamycin	0.19	0.19
Tcell	0.499	0.094
GMCSF	-0.288	0.636
IFNab	0.042	0.308
IFNg	0.791	0.537
IFNg_GMCSF1	0.949	0.688
Rv1432_day32	0.233	-0.428
Rv1565c_day32	-0.531	0.782
secA2_input	-0.454	-0.891
delta_Rv3594	-0.069	-0.571
delta_Rv3717	-1.0	-1.178
delta_Rv3811	0.033	-0.265
delta_Rv0954	0.181	-1.172
PonA1	0.208	-0.066
EccD1_KO	-0.743	-0.625
EspI_KO	-0.607	-0.331
PE35_KO	-1.199	-0.726
PPE68_KO	-0.602	-0.701
glycerol2	0.395	-0.084
lignocerate	0.619	-0.073
oleate	0.624	0.234
phosphatidylcholine	0.829	0.041
acetate	0.078	0.017
glucAc	0.095	-0.627
Rv0950ko	-0.208	-0.136
Rv1096ko	-1.161	-0.22
Rv3684ko	-0.737	-0.508
delta_otsA_trehalose	-0.32	1.428