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 Rv3159c/PPE53:

update plot	correlation	link to info on gene
Rv2307B/-	(cc=0.5294)	info on Rv2307B/-
Rv2957/-	(cc=0.499)	info on Rv2957/-
Rv1582c/-	(cc=0.4971)	info on Rv1582c/-
Rv1490/-	(cc=0.4881)	info on Rv1490/-
Rv3121/cyp141	(cc=0.488)	info on Rv3121/cyp141
Rv1917c/PPE34	(cc=0.487)	info on Rv1917c/PPE34
Rv3380c/-	(cc=0.4789)	info on Rv3380c/-
Rv3018c/PPE46	(cc=0.4698)	info on Rv3018c/PPE46
Rv1576c/-	(cc=0.4671)	info on Rv1576c/-
Rv3339c/icd1	(cc=0.4665)	info on Rv3339c/icd1

Correlation of Rv3159c/PPE53 with Rv2307B/-

Normalized LFCs for Rv3159c/PPE53:
(description and provenance of datasets)

	Rv3159c/PPE53	Rv2307B/-
Fe_supp_jason_reseq	0.499	0.226
low_pH_jason_reseq	0.025	0.539
NO_jason_reseq	0.63	-0.885
B6_jason_reseq	-0.405	-1.249
MHCII_jason_reseq	-0.015	-0.406
Isoniazid02	-0.812	-0.659
Rifampicin4	0.994	-0.653
Ethambutol3	1.429	3.588
Meropenem3	-0.349	-0.103
Vancomycin16	0.366	0.0
Rv2680_day32	0.779	0.816
H37Rv_KO_MarP	0.502	-0.099
hypoxia_3wks	-0.116	0.0
hypoxia_6wks	-0.04	-0.069
glycerol	-0.475	-0.332
cholesterol	0.44	-0.098
AJ	0.466	0.582
Bibs02	0.273	0.395
Bibs02c	-0.52	-0.399
BL6	0.835	0.053
BL6a	0.227	-0.484
BXD01	0.293	-0.469
BXD010	0.267	-1.557
BXD011	-0.149	-0.718
BXD03	0.337	0.493
BXD04	0.195	0.0
BXD05	0.418	0.266
BXD06	0.256	-0.254
BXD07	0.623	-0.543
BXD08	-0.111	-0.362
BXD09	0.405	-0.506
CAST	1.081	1.26
CCcont	0.249	-0.136
DS01	-0.048	-0.33
DS02	-0.09	0.309
DS04	0.631	0.519
DS0c	0.042	-0.781
GP01	0.058	-0.633
GP02	0.24	0.497
GP0c	0.113	-1.41
NOD	1.181	0.277
NZO	0.987	0.695
PWK	0.458	0.524
H37Rv_KO_CtpC	0.611	0.734
H37Rv_KO_CtpD	1.063	0.131
H37Rv_KO_Rv1272	0.5	-0.904
H37Rv_KO_SugABC	0.874	1.193
H37Rv_KO_MbtN	1.067	0.653
Trans05	0.671	0.282
macrophage_unactivated	0.129	-0.811
IL1	-0.59	-0.27
Rapamycin	-0.5	-1.617
Tcell	-0.101	-0.401
GMCSF	0.314	-0.586
IFNab	-0.493	-1.11
IFNg	-0.168	-0.329
IFNg_GMCSF1	-0.132	-0.591
Rv1432_day32	0.365	-0.378
Rv1565c_day32	0.03	0.0
secA2_input	0.185	-0.055
delta_Rv3594	0.375	1.459
delta_Rv3717	0.05	1.314
delta_Rv3811	0.262	1.083
delta_Rv0954	-0.425	0.112
PonA1	-0.112	0.901
EccD1_KO	-0.595	-0.201
EspI_KO	0.602	0.633
PE35_KO	0.785	-0.563
PPE68_KO	0.643	0.0
glycerol2	0.154	0.158
lignocerate	-0.222	0.035
oleate	0.553	0.122
phosphatidylcholine	0.237	0.375
acetate	-0.228	-0.204
glucAc	-0.361	-0.194
Rv0950ko	0.081	0.069
Rv1096ko	-0.838	-2.364
Rv3684ko	-0.946	-1.955
delta_otsA_trehalose	0.027	-3.005