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 Rv2496c/bkdB:

update plot	correlation	link to info on gene
Rv1430/PE16	(cc=0.5391)	info on Rv1430/PE16
Rv2857c/-	(cc=0.5223)	info on Rv2857c/-
Rv0397A/-	(cc=0.5208)	info on Rv0397A/-
Rv1551/plsB1	(cc=0.508)	info on Rv1551/plsB1
Rv1021/-	(cc=0.5078)	info on Rv1021/-
Rv1353c/-	(cc=0.4926)	info on Rv1353c/-
Rv1496/-	(cc=0.4913)	info on Rv1496/-
Rv1521/fadD25	(cc=0.4806)	info on Rv1521/fadD25
Rv1729c/-	(cc=0.4775)	info on Rv1729c/-
Rv1980c/mpt64	(cc=0.4734)	info on Rv1980c/mpt64

Correlation of Rv2496c/bkdB with Rv1496/-

Normalized LFCs for Rv2496c/bkdB:
(description and provenance of datasets)

	Rv2496c/bkdB	Rv1496/-
Fe_supp_jason_reseq	0.469	1.225
low_pH_jason_reseq	0.381	-0.172
NO_jason_reseq	1.197	-0.462
B6_jason_reseq	-1.586	-1.166
MHCII_jason_reseq	0.223	-1.939
Isoniazid02	0.135	1.441
Rifampicin4	-1.21	-0.379
Ethambutol3	0.22	1.459
Meropenem3	-0.789	0.184
Vancomycin16	-0.13	-0.289
Rv2680_day32	-0.05	0.208
H37Rv_KO_MarP	-0.354	-0.47
hypoxia_3wks	0.63	0.67
hypoxia_6wks	0.0	-0.299
glycerol	-1.463	0.186
cholesterol	-0.691	0.81
AJ	0.442	-1.002
Bibs02	-0.273	-0.152
Bibs02c	-1.375	-1.061
BL6	1.107	0.926
BL6a	0.198	-0.271
BXD01	1.094	0.692
BXD010	0.629	1.726
BXD011	0.448	0.963
BXD03	0.882	0.867
BXD04	1.131	2.068
BXD05	0.602	0.953
BXD06	0.535	0.514
BXD07	1.247	0.875
BXD08	0.253	1.377
BXD09	0.347	0.786
CAST	-1.23	-0.584
CCcont	0.917	1.924
DS01	-0.26	-1.138
DS02	-0.158	-2.568
DS04	-0.453	-1.436
DS0c	0.919	-1.403
GP01	0.188	2.198
GP02	0.617	0.113
GP0c	0.61	1.915
NOD	-0.428	-1.453
NZO	-0.144	-1.118
PWK	0.067	0.122
H37Rv_KO_CtpC	0.0	-0.379
H37Rv_KO_CtpD	0.65	1.685
H37Rv_KO_Rv1272	0.227	0.324
H37Rv_KO_SugABC	0.348	-0.641
H37Rv_KO_MbtN	1.484	1.89
Trans05	1.47	0.882
macrophage_unactivated	0.597	0.319
IL1	0.878	0.825
Rapamycin	0.973	1.126
Tcell	-1.007	0.31
GMCSF	0.89	1.516
IFNab	1.019	0.538
IFNg	0.505	1.761
IFNg_GMCSF1	0.0	0.789
Rv1432_day32	-0.055	0.0
Rv1565c_day32	0.231	0.058
secA2_input	-1.244	-0.873
delta_Rv3594	-0.122	-0.699
delta_Rv3717	-0.863	-0.162
delta_Rv3811	-0.379	0.251
delta_Rv0954	-0.886	-1.087
PonA1	-0.792	0.316
EccD1_KO	0.835	1.059
EspI_KO	0.588	-0.513
PE35_KO	0.601	0.318
PPE68_KO	1.171	0.512
glycerol2	0.238	-0.509
lignocerate	0.284	-0.061
oleate	1.259	0.323
phosphatidylcholine	0.49	0.141
acetate	-0.462	-0.042
glucAc	-0.586	-0.318
Rv0950ko	-0.172	1.173
Rv1096ko	0.477	0.875
Rv3684ko	0.675	1.13
delta_otsA_trehalose	-0.075	0.014