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 Rv1524/-

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

	Rv2991/-	Rv1524/-
Fe_supp_jason_reseq	0.101	-0.783
low_pH_jason_reseq	1.258	0.06
NO_jason_reseq	0.2	-0.247
B6_jason_reseq	-0.183	-0.041
MHCII_jason_reseq	-1.269	0.152
Isoniazid02	-0.028	0.076
Rifampicin4	0.152	-0.097
Ethambutol3	-0.235	0.0
Meropenem3	0.11	0.022
Vancomycin16	0.05	-0.048
Rv2680_day32	-0.256	0.947
H37Rv_KO_MarP	0.679	-0.102
hypoxia_3wks	-0.327	-0.096
hypoxia_6wks	-0.424	0.0
glycerol	-0.262	0.837
cholesterol	-0.402	0.322
AJ	1.573	0.666
Bibs02	-0.97	-0.359
Bibs02c	0.032	-0.591
BL6	1.067	0.41
BL6a	-0.28	0.106
BXD01	-0.082	-0.713
BXD010	0.471	0.634
BXD011	0.404	1.707
BXD03	0.582	0.893
BXD04	-0.327	-0.07
BXD05	1.426	0.222
BXD06	1.383	0.438
BXD07	0.505	0.697
BXD08	1.122	0.526
BXD09	1.091	0.683
CAST	0.447	0.184
CCcont	0.206	0.591
DS01	-0.474	0.157
DS02	0.17	0.28
DS04	-0.252	-0.731
DS0c	0.431	-1.188
GP01	-0.051	0.127
GP02	0.82	1.222
GP0c	0.213	0.087
NOD	2.182	1.295
NZO	0.579	-0.751
PWK	0.554	0.277
H37Rv_KO_CtpC	0.368	0.448
H37Rv_KO_CtpD	1.816	-0.918
H37Rv_KO_Rv1272	0.063	0.598
H37Rv_KO_SugABC	-0.275	0.066
H37Rv_KO_MbtN	-0.342	-0.255
Trans05	0.27	-0.393
macrophage_unactivated	0.417	0.54
IL1	-0.332	0.845
Rapamycin	0.559	0.657
Tcell	-0.808	0.961
GMCSF	0.055	0.451
IFNab	0.063	0.387
IFNg	0.526	0.158
IFNg_GMCSF1	1.194	0.927
Rv1432_day32	-0.454	-0.902
Rv1565c_day32	2.042	0.0
secA2_input	1.794	0.0
delta_Rv3594	-0.5	-0.918
delta_Rv3717	-1.112	-0.727
delta_Rv3811	0.167	-1.337
delta_Rv0954	-0.047	-1.273
PonA1	0.379	-0.885
EccD1_KO	0.266	1.128
EspI_KO	-0.445	-0.887
PE35_KO	0.341	0.245
PPE68_KO	0.339	0.134
glycerol2	0.041	0.499
lignocerate	1.369	1.595
oleate	-0.672	-1.874
phosphatidylcholine	0.665	0.368
acetate	1.564	1.892
glucAc	1.275	1.927
Rv0950ko	0.247	0.552
Rv1096ko	0.736	0.618
Rv3684ko	0.111	1.071
delta_otsA_trehalose	1.428	0.638