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 Rv2497c/bkdA:

update plot	correlation	link to info on gene
Rv3738c/PPE66	(cc=0.5361)	info on Rv3738c/PPE66
Rv0742/PE_PGRS8	(cc=0.5068)	info on Rv0742/PE_PGRS8
Rv2871/vapB43	(cc=0.4892)	info on Rv2871/vapB43
Rv3694c/-	(cc=0.4833)	info on Rv3694c/-
Rv3688c/-	(cc=0.4766)	info on Rv3688c/-
Rv1498c/-	(cc=0.4603)	info on Rv1498c/-
Rv2300c/-	(cc=0.4583)	info on Rv2300c/-
Rv1809/PPE33	(cc=0.456)	info on Rv1809/PPE33
Rv0397A/-	(cc=0.453)	info on Rv0397A/-
Rv2947c/pks15	(cc=0.4452)	info on Rv2947c/pks15

Correlation of Rv2497c/bkdA with Rv3688c/-

Normalized LFCs for Rv2497c/bkdA:
(description and provenance of datasets)

	Rv2497c/bkdA	Rv3688c/-
Fe_supp_jason_reseq	-0.297	-0.737
low_pH_jason_reseq	0.244	0.5
NO_jason_reseq	0.36	0.21
B6_jason_reseq	-1.575	-0.529
MHCII_jason_reseq	0.011	0.319
Isoniazid02	-1.077	-0.952
Rifampicin4	0.263	-0.439
Ethambutol3	-1.058	-0.725
Meropenem3	-0.461	-0.383
Vancomycin16	-1.035	-0.862
Rv2680_day32	-0.473	0.57
H37Rv_KO_MarP	-0.144	0.233
hypoxia_3wks	0.634	0.941
hypoxia_6wks	-0.578	0.662
glycerol	-1.842	-1.868
cholesterol	0.311	-0.148
AJ	-0.062	0.062
Bibs02	0.432	-0.011
Bibs02c	0.426	0.0
BL6	0.255	0.439
BL6a	0.666	0.323
BXD01	0.147	-0.596
BXD010	0.491	0.178
BXD011	0.476	-0.205
BXD03	-0.389	0.358
BXD04	-0.334	0.192
BXD05	0.528	0.602
BXD06	0.342	0.629
BXD07	0.641	0.204
BXD08	0.118	0.455
BXD09	0.732	0.25
CAST	-1.006	-0.057
CCcont	0.444	0.036
DS01	0.238	-0.125
DS02	-0.375	-0.55
DS04	0.125	-0.264
DS0c	0.644	0.668
GP01	0.682	-0.072
GP02	0.178	0.937
GP0c	0.192	-0.261
NOD	-0.218	-0.731
NZO	0.103	0.09
PWK	0.503	0.578
H37Rv_KO_CtpC	1.407	0.068
H37Rv_KO_CtpD	0.299	-0.092
H37Rv_KO_Rv1272	1.469	-0.197
H37Rv_KO_SugABC	1.395	1.124
H37Rv_KO_MbtN	0.21	0.108
Trans05	0.92	0.402
macrophage_unactivated	1.111	0.038
IL1	0.676	-0.036
Rapamycin	0.246	-0.338
Tcell	0.668	0.062
GMCSF	0.784	0.401
IFNab	0.828	-0.181
IFNg	1.053	0.061
IFNg_GMCSF1	0.49	0.443
Rv1432_day32	-0.117	-0.694
Rv1565c_day32	-0.542	-1.243
secA2_input	0.509	-0.016
delta_Rv3594	-0.24	-0.505
delta_Rv3717	0.305	-0.842
delta_Rv3811	-0.214	-0.44
delta_Rv0954	-0.669	-0.37
PonA1	-0.777	0.651
EccD1_KO	-0.51	-0.125
EspI_KO	-1.072	-0.268
PE35_KO	0.184	-0.98
PPE68_KO	0.422	-1.075
glycerol2	0.581	0.841
lignocerate	1.132	0.784
oleate	1.466	0.564
phosphatidylcholine	0.753	1.006
acetate	0.775	0.231
glucAc	0.0	0.359
Rv0950ko	-0.172	0.305
Rv1096ko	0.066	-0.112
Rv3684ko	0.0	0.046
delta_otsA_trehalose	-0.184	1.278