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 Rv1498c/-

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

	Rv2497c/bkdA	Rv1498c/-
Fe_supp_jason_reseq	-0.297	1.557
low_pH_jason_reseq	0.244	0.499
NO_jason_reseq	0.36	0.339
B6_jason_reseq	-1.575	-0.235
MHCII_jason_reseq	0.011	-0.081
Isoniazid02	-1.077	-1.26
Rifampicin4	0.263	0.23
Ethambutol3	-1.058	-1.16
Meropenem3	-0.461	-1.318
Vancomycin16	-1.035	-0.806
Rv2680_day32	-0.473	0.016
H37Rv_KO_MarP	-0.144	-0.631
hypoxia_3wks	0.634	0.443
hypoxia_6wks	-0.578	0.092
glycerol	-1.842	-0.064
cholesterol	0.311	0.441
AJ	-0.062	0.402
Bibs02	0.432	0.525
Bibs02c	0.426	-0.189
BL6	0.255	0.969
BL6a	0.666	0.65
BXD01	0.147	0.548
BXD010	0.491	1.26
BXD011	0.476	1.351
BXD03	-0.389	0.869
BXD04	-0.334	0.713
BXD05	0.528	1.417
BXD06	0.342	0.962
BXD07	0.641	0.97
BXD08	0.118	0.654
BXD09	0.732	0.855
CAST	-1.006	-0.35
CCcont	0.444	0.82
DS01	0.238	0.517
DS02	-0.375	-0.391
DS04	0.125	0.817
DS0c	0.644	0.434
GP01	0.682	0.704
GP02	0.178	0.51
GP0c	0.192	0.225
NOD	-0.218	1.538
NZO	0.103	0.548
PWK	0.503	0.644
H37Rv_KO_CtpC	1.407	1.414
H37Rv_KO_CtpD	0.299	0.01
H37Rv_KO_Rv1272	1.469	0.942
H37Rv_KO_SugABC	1.395	1.369
H37Rv_KO_MbtN	0.21	0.905
Trans05	0.92	1.564
macrophage_unactivated	1.111	0.404
IL1	0.676	0.08
Rapamycin	0.246	0.015
Tcell	0.668	0.384
GMCSF	0.784	-0.071
IFNab	0.828	0.082
IFNg	1.053	0.633
IFNg_GMCSF1	0.49	0.54
Rv1432_day32	-0.117	0.282
Rv1565c_day32	-0.542	0.646
secA2_input	0.509	-0.233
delta_Rv3594	-0.24	-0.205
delta_Rv3717	0.305	-0.238
delta_Rv3811	-0.214	-0.691
delta_Rv0954	-0.669	-0.702
PonA1	-0.777	-0.268
EccD1_KO	-0.51	0.865
EspI_KO	-1.072	0.85
PE35_KO	0.184	1.397
PPE68_KO	0.422	1.667
glycerol2	0.581	0.252
lignocerate	1.132	0.818
oleate	1.466	0.109
phosphatidylcholine	0.753	0.374
acetate	0.775	0.332
glucAc	0.0	0.76
Rv0950ko	-0.172	0.241
Rv1096ko	0.066	-0.908
Rv3684ko	0.0	-0.301
delta_otsA_trehalose	-0.184	-1.361