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 Rv2871/vapB43

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

	Rv2497c/bkdA	Rv2871/vapB43
Fe_supp_jason_reseq	-0.297	-0.188
low_pH_jason_reseq	0.244	-0.571
NO_jason_reseq	0.36	0.378
B6_jason_reseq	-1.575	-1.287
MHCII_jason_reseq	0.011	-0.535
Isoniazid02	-1.077	-0.438
Rifampicin4	0.263	0.577
Ethambutol3	-1.058	0.387
Meropenem3	-0.461	0.0
Vancomycin16	-1.035	0.215
Rv2680_day32	-0.473	0.554
H37Rv_KO_MarP	-0.144	1.098
hypoxia_3wks	0.634	-1.013
hypoxia_6wks	-0.578	-0.965
glycerol	-1.842	-1.788
cholesterol	0.311	0.054
AJ	-0.062	1.356
Bibs02	0.432	-1.325
Bibs02c	0.426	-1.091
BL6	0.255	0.952
BL6a	0.666	1.158
BXD01	0.147	1.412
BXD010	0.491	0.047
BXD011	0.476	0.947
BXD03	-0.389	0.098
BXD04	-0.334	0.584
BXD05	0.528	0.603
BXD06	0.342	1.196
BXD07	0.641	0.479
BXD08	0.118	0.75
BXD09	0.732	0.881
CAST	-1.006	-0.37
CCcont	0.444	2.347
DS01	0.238	-0.83
DS02	-0.375	-2.339
DS04	0.125	0.207
DS0c	0.644	0.809
GP01	0.682	0.466
GP02	0.178	-0.603
GP0c	0.192	0.223
NOD	-0.218	-0.91
NZO	0.103	-0.41
PWK	0.503	1.309
H37Rv_KO_CtpC	1.407	1.905
H37Rv_KO_CtpD	0.299	-0.204
H37Rv_KO_Rv1272	1.469	0.995
H37Rv_KO_SugABC	1.395	2.157
H37Rv_KO_MbtN	0.21	2.291
Trans05	0.92	0.0
macrophage_unactivated	1.111	1.689
IL1	0.676	0.795
Rapamycin	0.246	1.826
Tcell	0.668	0.456
GMCSF	0.784	1.135
IFNab	0.828	0.0
IFNg	1.053	1.938
IFNg_GMCSF1	0.49	-0.189
Rv1432_day32	-0.117	0.763
Rv1565c_day32	-0.542	0.684
secA2_input	0.509	0.286
delta_Rv3594	-0.24	-1.042
delta_Rv3717	0.305	-0.327
delta_Rv3811	-0.214	-1.054
delta_Rv0954	-0.669	-1.105
PonA1	-0.777	-1.626
EccD1_KO	-0.51	-0.069
EspI_KO	-1.072	1.289
PE35_KO	0.184	-1.645
PPE68_KO	0.422	-0.656
glycerol2	0.581	1.361
lignocerate	1.132	1.32
oleate	1.466	0.746
phosphatidylcholine	0.753	1.188
acetate	0.775	2.08
glucAc	0.0	1.459
Rv0950ko	-0.172	-0.89
Rv1096ko	0.066	-0.247
Rv3684ko	0.0	1.225
delta_otsA_trehalose	-0.184	0.073