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 Rv1752/-:

update plot	correlation	link to info on gene
Rv1616/-	(cc=0.6756)	info on Rv1616/-
Rv1059/-	(cc=0.6077)	info on Rv1059/-
Rv0766c/cyp123	(cc=0.5917)	info on Rv0766c/cyp123
Rv1116/-	(cc=0.5785)	info on Rv1116/-
Rv3125c/PPE49	(cc=0.5649)	info on Rv3125c/PPE49
Rv1521/fadD25	(cc=0.5647)	info on Rv1521/fadD25
Rv3533c/PPE62	(cc=0.5595)	info on Rv3533c/PPE62
Rv0844c/narL	(cc=0.5574)	info on Rv0844c/narL
Rv1386/PE15	(cc=0.5481)	info on Rv1386/PE15
Rv1551/plsB1	(cc=0.5462)	info on Rv1551/plsB1

Correlation of Rv1752/- with Rv0766c/cyp123

Normalized LFCs for Rv1752/-:
(description and provenance of datasets)

	Rv1752/-	Rv0766c/cyp123
Fe_supp_jason_reseq	0.898	-0.262
low_pH_jason_reseq	-0.161	-0.462
NO_jason_reseq	-0.764	-0.53
B6_jason_reseq	-0.729	-1.009
MHCII_jason_reseq	-0.549	-0.162
Isoniazid02	-0.434	-0.693
Rifampicin4	0.555	0.514
Ethambutol3	1.171	-0.113
Meropenem3	0.194	-0.359
Vancomycin16	0.0	-0.183
Rv2680_day32	-2.199	-1.396
H37Rv_KO_MarP	0.524	0.409
hypoxia_3wks	2.444	0.319
hypoxia_6wks	2.717	0.474
glycerol	1.779	-0.237
cholesterol	0.643	-0.134
AJ	1.076	0.101
Bibs02	0.404	0.118
Bibs02c	-1.94	0.091
BL6	1.559	1.124
BL6a	2.314	0.399
BXD01	3.174	0.884
BXD010	1.471	0.371
BXD011	2.332	2.108
BXD03	2.639	0.029
BXD04	3.421	1.373
BXD05	3.019	0.412
BXD06	3.229	0.724
BXD07	2.882	0.988
BXD08	2.391	1.021
BXD09	2.702	1.079
CAST	0.779	1.156
CCcont	1.774	0.355
DS01	-1.437	0.0
DS02	-0.989	-0.099
DS04	-0.544	0.749
DS0c	0.368	0.966
GP01	2.24	-0.247
GP02	3.888	0.137
GP0c	2.7	0.772
NOD	-0.142	0.412
NZO	1.621	-0.285
PWK	0.117	0.395
H37Rv_KO_CtpC	2.829	1.504
H37Rv_KO_CtpD	1.947	2.358
H37Rv_KO_Rv1272	1.77	-0.817
H37Rv_KO_SugABC	2.44	1.545
H37Rv_KO_MbtN	1.34	1.653
Trans05	-0.315	-0.918
macrophage_unactivated	1.073	0.0
IL1	0.234	-0.543
Rapamycin	1.197	0.381
Tcell	2.587	0.466
GMCSF	0.504	-0.549
IFNab	-0.577	0.314
IFNg	-0.796	0.732
IFNg_GMCSF1	-0.346	-0.575
Rv1432_day32	0.18	0.143
Rv1565c_day32	-1.777	-0.033
secA2_input	0.44	-0.18
delta_Rv3594	0.646	-0.298
delta_Rv3717	-0.608	-1.094
delta_Rv3811	-0.802	-0.882
delta_Rv0954	1.056	-1.478
PonA1	-0.6	0.417
EccD1_KO	0.842	0.506
EspI_KO	0.625	0.257
PE35_KO	1.808	0.263
PPE68_KO	1.414	0.358
glycerol2	-0.336	-0.404
lignocerate	-1.251	-0.856
oleate	0.043	-0.016
phosphatidylcholine	-0.319	-0.183
acetate	-2.123	-1.049
glucAc	-1.959	-0.91
Rv0950ko	0.142	0.302
Rv1096ko	1.131	-0.127
Rv3684ko	-0.976	-0.422
delta_otsA_trehalose	-2.184	-1.353