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 Rv1482c/-:

update plot	correlation	link to info on gene
Rv1215c/-	(cc=0.6263)	info on Rv1215c/-
Rv1616/-	(cc=0.5739)	info on Rv1616/-
Rv0149/-	(cc=0.5435)	info on Rv0149/-
Rv1164/narI	(cc=0.5358)	info on Rv1164/narI
Rv1816/-	(cc=0.5273)	info on Rv1816/-
Rv2305/-	(cc=0.5035)	info on Rv2305/-
Rv1831/-	(cc=0.4994)	info on Rv1831/-
Rv3398c/idsA1	(cc=0.4962)	info on Rv3398c/idsA1
Rv2389c/rpfD	(cc=0.4939)	info on Rv2389c/rpfD
Rv2451/-	(cc=0.4923)	info on Rv2451/-

Correlation of Rv1482c/- with Rv2305/-

Normalized LFCs for Rv1482c/-:
(description and provenance of datasets)

	Rv1482c/-	Rv2305/-
Fe_supp_jason_reseq	0.286	0.379
low_pH_jason_reseq	-0.639	-0.346
NO_jason_reseq	0.417	-1.021
B6_jason_reseq	-0.856	0.074
MHCII_jason_reseq	-1.002	0.138
Isoniazid02	-0.009	0.495
Rifampicin4	0.173	1.21
Ethambutol3	1.923	3.078
Meropenem3	1.896	1.479
Vancomycin16	0.305	0.623
Rv2680_day32	0.067	0.324
H37Rv_KO_MarP	0.024	0.03
hypoxia_3wks	0.231	0.439
hypoxia_6wks	-0.013	-0.284
glycerol	-0.257	-0.238
cholesterol	-0.321	0.04
AJ	0.039	1.012
Bibs02	-0.729	-0.926
Bibs02c	-0.061	-0.079
BL6	0.836	0.122
BL6a	0.509	0.673
BXD01	0.713	0.829
BXD010	0.887	0.928
BXD011	0.125	0.594
BXD03	0.825	0.606
BXD04	0.434	0.152
BXD05	0.979	0.83
BXD06	0.276	0.523
BXD07	0.398	0.896
BXD08	0.348	0.547
BXD09	0.482	0.737
CAST	-0.264	0.395
CCcont	0.1	0.268
DS01	-0.732	0.108
DS02	-0.452	0.618
DS04	0.427	-0.734
DS0c	-0.222	-0.625
GP01	-0.306	-0.127
GP02	0.225	1.366
GP0c	0.286	0.591
NOD	-0.187	-0.063
NZO	0.477	0.038
PWK	1.599	0.209
H37Rv_KO_CtpC	0.9	0.824
H37Rv_KO_CtpD	0.273	-1.397
H37Rv_KO_Rv1272	0.552	-0.182
H37Rv_KO_SugABC	0.339	0.413
H37Rv_KO_MbtN	0.431	-0.144
Trans05	1.091	2.35
macrophage_unactivated	-0.36	0.874
IL1	0.344	1.258
Rapamycin	-0.144	0.706
Tcell	0.551	-0.427
GMCSF	0.605	1.119
IFNab	0.121	1.249
IFNg	0.224	1.411
IFNg_GMCSF1	0.842	0.377
Rv1432_day32	1.348	0.656
Rv1565c_day32	0.619	1.096
secA2_input	-0.791	0.9
delta_Rv3594	-0.552	0.688
delta_Rv3717	-0.644	0.011
delta_Rv3811	-0.761	-0.013
delta_Rv0954	-0.652	-0.727
PonA1	0.016	-0.931
EccD1_KO	1.181	0.595
EspI_KO	0.65	0.876
PE35_KO	0.875	1.461
PPE68_KO	0.873	1.037
glycerol2	-0.328	-0.572
lignocerate	-0.412	-0.876
oleate	0.388	0.013
phosphatidylcholine	-0.146	-0.41
acetate	-0.818	-0.748
glucAc	-0.968	-1.269
Rv0950ko	0.323	0.0
Rv1096ko	0.036	0.139
Rv3684ko	0.35	0.121
delta_otsA_trehalose	-1.002	0.863