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 Rv2991/-:

update plot	correlation	link to info on gene
Rv2723/-	(cc=0.4636)	info on Rv2723/-
Rv0499/-	(cc=0.4526)	info on Rv0499/-
Rv1874/-	(cc=0.4023)	info on Rv1874/-
Rv3064c/-	(cc=0.3878)	info on Rv3064c/-
Rv1583c/-	(cc=0.38)	info on Rv1583c/-
Rv1524/-	(cc=0.38)	info on Rv1524/-
Rv2775/-	(cc=0.3789)	info on Rv2775/-
Rv1585c/-	(cc=0.3729)	info on Rv1585c/-
Rv1530/adh	(cc=0.3559)	info on Rv1530/adh
Rv0345/-	(cc=0.3489)	info on Rv0345/-

Correlation of Rv2991/- with Rv2775/-

Normalized LFCs for Rv2991/-:
(description and provenance of datasets)

	Rv2991/-	Rv2775/-
Fe_supp_jason_reseq	0.101	0.466
low_pH_jason_reseq	1.258	-0.037
NO_jason_reseq	0.2	-0.977
B6_jason_reseq	-0.183	0.469
MHCII_jason_reseq	-1.269	-0.364
Isoniazid02	-0.028	-0.389
Rifampicin4	0.152	-0.038
Ethambutol3	-0.235	-0.276
Meropenem3	0.11	-1.548
Vancomycin16	0.05	-0.127
Rv2680_day32	-0.256	-0.205
H37Rv_KO_MarP	0.679	-0.666
hypoxia_3wks	-0.327	-0.817
hypoxia_6wks	-0.424	0.058
glycerol	-0.262	-1.814
cholesterol	-0.402	-1.544
AJ	1.573	0.474
Bibs02	-0.97	-1.113
Bibs02c	0.032	-0.1
BL6	1.067	0.246
BL6a	-0.28	0.595
BXD01	-0.082	0.083
BXD010	0.471	1.009
BXD011	0.404	0.952
BXD03	0.582	0.569
BXD04	-0.327	0.432
BXD05	1.426	2.161
BXD06	1.383	1.25
BXD07	0.505	0.675
BXD08	1.122	0.499
BXD09	1.091	0.951
CAST	0.447	0.592
CCcont	0.206	0.59
DS01	-0.474	0.994
DS02	0.17	-0.378
DS04	-0.252	0.037
DS0c	0.431	-0.192
GP01	-0.051	1.913
GP02	0.82	0.55
GP0c	0.213	1.296
NOD	2.182	1.394
NZO	0.579	0.162
PWK	0.554	1.047
H37Rv_KO_CtpC	0.368	0.599
H37Rv_KO_CtpD	1.816	1.142
H37Rv_KO_Rv1272	0.063	1.787
H37Rv_KO_SugABC	-0.275	1.287
H37Rv_KO_MbtN	-0.342	0.538
Trans05	0.27	1.467
macrophage_unactivated	0.417	0.524
IL1	-0.332	-0.35
Rapamycin	0.559	0.964
Tcell	-0.808	-0.775
GMCSF	0.055	0.525
IFNab	0.063	0.747
IFNg	0.526	0.083
IFNg_GMCSF1	1.194	0.019
Rv1432_day32	-0.454	0.113
Rv1565c_day32	2.042	0.199
secA2_input	1.794	0.172
delta_Rv3594	-0.5	-0.812
delta_Rv3717	-1.112	-1.117
delta_Rv3811	0.167	-1.056
delta_Rv0954	-0.047	-1.181
PonA1	0.379	-2.209
EccD1_KO	0.266	0.506
EspI_KO	-0.445	1.269
PE35_KO	0.341	1.502
PPE68_KO	0.339	1.574
glycerol2	0.041	0.0
lignocerate	1.369	0.935
oleate	-0.672	-1.208
phosphatidylcholine	0.665	0.629
acetate	1.564	0.469
glucAc	1.275	0.563
Rv0950ko	0.247	0.389
Rv1096ko	0.736	0.178
Rv3684ko	0.111	-0.098
delta_otsA_trehalose	1.428	-0.085