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 Rv0397A/-

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

	Rv2497c/bkdA	Rv0397A/-
Fe_supp_jason_reseq	-0.297	0.655
low_pH_jason_reseq	0.244	-2.044
NO_jason_reseq	0.36	0.108
B6_jason_reseq	-1.575	-1.253
MHCII_jason_reseq	0.011	-0.813
Isoniazid02	-1.077	-2.242
Rifampicin4	0.263	-2.071
Ethambutol3	-1.058	-1.31
Meropenem3	-0.461	-1.388
Vancomycin16	-1.035	-1.464
Rv2680_day32	-0.473	-2.129
H37Rv_KO_MarP	-0.144	0.557
hypoxia_3wks	0.634	0.371
hypoxia_6wks	-0.578	-0.209
glycerol	-1.842	-0.837
cholesterol	0.311	-1.69
AJ	-0.062	0.514
Bibs02	0.432	-0.034
Bibs02c	0.426	-1.052
BL6	0.255	0.714
BL6a	0.666	0.696
BXD01	0.147	1.016
BXD010	0.491	1.88
BXD011	0.476	2.276
BXD03	-0.389	1.3
BXD04	-0.334	1.568
BXD05	0.528	0.473
BXD06	0.342	1.729
BXD07	0.641	1.667
BXD08	0.118	0.335
BXD09	0.732	1.569
CAST	-1.006	-1.23
CCcont	0.444	1.256
DS01	0.238	0.132
DS02	-0.375	1.404
DS04	0.125	-1.098
DS0c	0.644	0.933
GP01	0.682	1.24
GP02	0.178	1.347
GP0c	0.192	-0.157
NOD	-0.218	-0.867
NZO	0.103	-1.263
PWK	0.503	1.346
H37Rv_KO_CtpC	1.407	1.657
H37Rv_KO_CtpD	0.299	-1.275
H37Rv_KO_Rv1272	1.469	2.524
H37Rv_KO_SugABC	1.395	0.293
H37Rv_KO_MbtN	0.21	1.94
Trans05	0.92	1.93
macrophage_unactivated	1.111	0.477
IL1	0.676	0.303
Rapamycin	0.246	0.908
Tcell	0.668	-0.036
GMCSF	0.784	1.13
IFNab	0.828	0.762
IFNg	1.053	-0.516
IFNg_GMCSF1	0.49	0.321
Rv1432_day32	-0.117	-0.107
Rv1565c_day32	-0.542	0.144
secA2_input	0.509	0.803
delta_Rv3594	-0.24	-1.025
delta_Rv3717	0.305	-1.007
delta_Rv3811	-0.214	-0.329
delta_Rv0954	-0.669	-1.194
PonA1	-0.777	-0.792
EccD1_KO	-0.51	-1.108
EspI_KO	-1.072	-0.106
PE35_KO	0.184	-0.143
PPE68_KO	0.422	-0.486
glycerol2	0.581	-0.311
lignocerate	1.132	-1.053
oleate	1.466	0.133
phosphatidylcholine	0.753	-0.276
acetate	0.775	-0.349
glucAc	0.0	-0.937
Rv0950ko	-0.172	0.286
Rv1096ko	0.066	0.247
Rv3684ko	0.0	0.092
delta_otsA_trehalose	-0.184	0.564