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 Rv2584c/apt:

update plot	correlation	link to info on gene
Rv1059/-	(cc=0.6684)	info on Rv1059/-
Rv3150/nuoF	(cc=0.6665)	info on Rv3150/nuoF
Rv2430c/PPE41	(cc=0.6346)	info on Rv2430c/PPE41
Rv2569c/-	(cc=0.6256)	info on Rv2569c/-
Rv3864/espE	(cc=0.6219)	info on Rv3864/espE
Rv3152/nuoH	(cc=0.6182)	info on Rv3152/nuoH
Rv0059/-	(cc=0.6153)	info on Rv0059/-
Rv0260c/-	(cc=0.6146)	info on Rv0260c/-
Rv0502/-	(cc=0.6133)	info on Rv0502/-
Rv3153/nuoI	(cc=0.6126)	info on Rv3153/nuoI

Correlation of Rv2584c/apt with Rv3150/nuoF

Normalized LFCs for Rv2584c/apt:
(description and provenance of datasets)

	Rv2584c/apt	Rv3150/nuoF
Fe_supp_jason_reseq	-0.227	-1.514
low_pH_jason_reseq	0.565	-0.313
NO_jason_reseq	0.404	-0.252
B6_jason_reseq	-0.929	-1.087
MHCII_jason_reseq	-1.215	-1.509
Isoniazid02	-0.808	0.611
Rifampicin4	-0.146	0.282
Ethambutol3	-0.59	-0.595
Meropenem3	-0.443	-0.847
Vancomycin16	-0.268	-0.196
Rv2680_day32	0.892	0.266
H37Rv_KO_MarP	-0.556	-0.246
hypoxia_3wks	0.738	1.097
hypoxia_6wks	1.046	0.754
glycerol	0.758	-0.471
cholesterol	-0.069	-0.216
AJ	0.81	-0.983
Bibs02	1.106	0.55
Bibs02c	0.932	-0.23
BL6	0.958	1.845
BL6a	1.499	2.251
BXD01	0.868	1.864
BXD010	1.16	2.266
BXD011	0.701	2.05
BXD03	1.101	2.177
BXD04	1.281	2.337
BXD05	1.845	2.126
BXD06	1.349	2.045
BXD07	1.389	2.3
BXD08	1.048	2.274
BXD09	1.278	2.374
CAST	0.576	0.506
CCcont	1.444	1.451
DS01	0.274	0.583
DS02	0.12	0.147
DS04	-0.471	0.426
DS0c	0.511	0.969
GP01	0.774	0.715
GP02	0.966	0.875
GP0c	1.337	1.092
NOD	-0.042	-0.838
NZO	0.407	0.38
PWK	0.658	-0.142
H37Rv_KO_CtpC	0.281	1.463
H37Rv_KO_CtpD	1.793	2.661
H37Rv_KO_Rv1272	1.014	1.929
H37Rv_KO_SugABC	1.26	1.426
H37Rv_KO_MbtN	0.707	1.537
Trans05	1.018	1.798
macrophage_unactivated	0.619	0.284
IL1	0.697	0.267
Rapamycin	0.893	0.365
Tcell	0.228	0.746
GMCSF	2.017	0.388
IFNab	0.931	1.69
IFNg	-0.013	-0.302
IFNg_GMCSF1	0.264	0.145
Rv1432_day32	0.374	0.568
Rv1565c_day32	0.041	-0.208
secA2_input	-1.75	-0.116
delta_Rv3594	0.347	0.392
delta_Rv3717	-0.422	0.299
delta_Rv3811	-0.207	0.094
delta_Rv0954	-0.433	-0.057
PonA1	-0.406	-0.39
EccD1_KO	-0.977	-0.474
EspI_KO	-0.436	-0.177
PE35_KO	-0.688	-0.467
PPE68_KO	-0.611	0.0
glycerol2	0.378	1.866
lignocerate	0.226	-0.192
oleate	0.55	2.076
phosphatidylcholine	0.378	-0.221
acetate	0.484	-0.263
glucAc	-0.133	0.587
Rv0950ko	-0.703	0.311
Rv1096ko	-0.401	0.639
Rv3684ko	-1.117	0.098
delta_otsA_trehalose	-0.167	0.965