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 Rv0742/PE_PGRS8

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

	Rv2497c/bkdA	Rv0742/PE_PGRS8
Fe_supp_jason_reseq	-0.297	-1.888
low_pH_jason_reseq	0.244	0.562
NO_jason_reseq	0.36	-0.538
B6_jason_reseq	-1.575	-1.831
MHCII_jason_reseq	0.011	-2.072
Isoniazid02	-1.077	-0.065
Rifampicin4	0.263	1.616
Ethambutol3	-1.058	-0.044
Meropenem3	-0.461	0.386
Vancomycin16	-1.035	-0.024
Rv2680_day32	-0.473	0.605
H37Rv_KO_MarP	-0.144	0.477
hypoxia_3wks	0.634	0.833
hypoxia_6wks	-0.578	-1.088
glycerol	-1.842	0.045
cholesterol	0.311	-0.366
AJ	-0.062	0.128
Bibs02	0.432	-0.36
Bibs02c	0.426	0.799
BL6	0.255	1.464
BL6a	0.666	1.39
BXD01	0.147	1.329
BXD010	0.491	0.519
BXD011	0.476	1.026
BXD03	-0.389	1.328
BXD04	-0.334	0.0
BXD05	0.528	1.827
BXD06	0.342	0.571
BXD07	0.641	0.83
BXD08	0.118	1.234
BXD09	0.732	1.298
CAST	-1.006	1.053
CCcont	0.444	1.218
DS01	0.238	0.587
DS02	-0.375	0.21
DS04	0.125	0.266
DS0c	0.644	-0.341
GP01	0.682	2.262
GP02	0.178	1.611
GP0c	0.192	1.126
NOD	-0.218	-0.6
NZO	0.103	-0.448
PWK	0.503	0.573
H37Rv_KO_CtpC	1.407	1.092
H37Rv_KO_CtpD	0.299	0.494
H37Rv_KO_Rv1272	1.469	0.94
H37Rv_KO_SugABC	1.395	0.915
H37Rv_KO_MbtN	0.21	0.937
Trans05	0.92	1.328
macrophage_unactivated	1.111	0.922
IL1	0.676	0.581
Rapamycin	0.246	0.703
Tcell	0.668	0.766
GMCSF	0.784	1.328
IFNab	0.828	0.287
IFNg	1.053	-0.561
IFNg_GMCSF1	0.49	0.229
Rv1432_day32	-0.117	1.042
Rv1565c_day32	-0.542	-1.703
secA2_input	0.509	1.249
delta_Rv3594	-0.24	-0.405
delta_Rv3717	0.305	-0.447
delta_Rv3811	-0.214	-0.428
delta_Rv0954	-0.669	-0.868
PonA1	-0.777	-2.069
EccD1_KO	-0.51	-0.257
EspI_KO	-1.072	-0.807
PE35_KO	0.184	-0.166
PPE68_KO	0.422	0.0
glycerol2	0.581	0.792
lignocerate	1.132	0.737
oleate	1.466	1.311
phosphatidylcholine	0.753	1.045
acetate	0.775	0.359
glucAc	0.0	0.254
Rv0950ko	-0.172	-0.205
Rv1096ko	0.066	-0.54
Rv3684ko	0.0	-0.793
delta_otsA_trehalose	-0.184	-0.388