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 Rv2723/-

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

	Rv2991/-	Rv2723/-
Fe_supp_jason_reseq	0.101	-0.882
low_pH_jason_reseq	1.258	-0.838
NO_jason_reseq	0.2	1.344
B6_jason_reseq	-0.183	-1.475
MHCII_jason_reseq	-1.269	-1.556
Isoniazid02	-0.028	-0.224
Rifampicin4	0.152	-0.504
Ethambutol3	-0.235	0.815
Meropenem3	0.11	-1.035
Vancomycin16	0.05	-1.005
Rv2680_day32	-0.256	-1.107
H37Rv_KO_MarP	0.679	-0.309
hypoxia_3wks	-0.327	-1.3
hypoxia_6wks	-0.424	-0.965
glycerol	-0.262	-0.434
cholesterol	-0.402	-1.074
AJ	1.573	0.311
Bibs02	-0.97	-1.155
Bibs02c	0.032	-1.366
BL6	1.067	0.223
BL6a	-0.28	-0.344
BXD01	-0.082	0.037
BXD010	0.471	0.773
BXD011	0.404	0.488
BXD03	0.582	0.712
BXD04	-0.327	0.916
BXD05	1.426	0.741
BXD06	1.383	1.031
BXD07	0.505	0.547
BXD08	1.122	0.275
BXD09	1.091	0.745
CAST	0.447	0.936
CCcont	0.206	0.075
DS01	-0.474	-1.619
DS02	0.17	-0.759
DS04	-0.252	-0.572
DS0c	0.431	-0.723
GP01	-0.051	-1.021
GP02	0.82	0.354
GP0c	0.213	-0.444
NOD	2.182	0.973
NZO	0.579	0.692
PWK	0.554	1.432
H37Rv_KO_CtpC	0.368	0.845
H37Rv_KO_CtpD	1.816	1.413
H37Rv_KO_Rv1272	0.063	0.224
H37Rv_KO_SugABC	-0.275	-0.133
H37Rv_KO_MbtN	-0.342	-0.402
Trans05	0.27	0.415
macrophage_unactivated	0.417	-0.322
IL1	-0.332	-0.122
Rapamycin	0.559	-1.04
Tcell	-0.808	0.186
GMCSF	0.055	0.032
IFNab	0.063	-0.502
IFNg	0.526	0.655
IFNg_GMCSF1	1.194	0.581
Rv1432_day32	-0.454	-1.967
Rv1565c_day32	2.042	-0.798
secA2_input	1.794	0.333
delta_Rv3594	-0.5	-1.361
delta_Rv3717	-1.112	-2.117
delta_Rv3811	0.167	-1.966
delta_Rv0954	-0.047	0.142
PonA1	0.379	0.297
EccD1_KO	0.266	0.0
EspI_KO	-0.445	0.157
PE35_KO	0.341	-0.388
PPE68_KO	0.339	-0.115
glycerol2	0.041	-0.13
lignocerate	1.369	-0.628
oleate	-0.672	0.641
phosphatidylcholine	0.665	0.773
acetate	1.564	-0.263
glucAc	1.275	-0.396
Rv0950ko	0.247	0.22
Rv1096ko	0.736	-1.071
Rv3684ko	0.111	-0.134
delta_otsA_trehalose	1.428	1.112