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 Rv1809/PPE33

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

	Rv2497c/bkdA	Rv1809/PPE33
Fe_supp_jason_reseq	-0.297	-0.895
low_pH_jason_reseq	0.244	0.0
NO_jason_reseq	0.36	-1.79
B6_jason_reseq	-1.575	-2.074
MHCII_jason_reseq	0.011	-1.223
Isoniazid02	-1.077	0.566
Rifampicin4	0.263	-0.084
Ethambutol3	-1.058	-0.299
Meropenem3	-0.461	0.585
Vancomycin16	-1.035	0.22
Rv2680_day32	-0.473	-0.943
H37Rv_KO_MarP	-0.144	0.12
hypoxia_3wks	0.634	0.124
hypoxia_6wks	-0.578	-0.027
glycerol	-1.842	-0.427
cholesterol	0.311	0.34
AJ	-0.062	-0.424
Bibs02	0.432	0.607
Bibs02c	0.426	0.881
BL6	0.255	0.683
BL6a	0.666	0.646
BXD01	0.147	0.211
BXD010	0.491	0.325
BXD011	0.476	0.089
BXD03	-0.389	0.409
BXD04	-0.334	0.501
BXD05	0.528	0.892
BXD06	0.342	0.305
BXD07	0.641	0.126
BXD08	0.118	0.141
BXD09	0.732	0.179
CAST	-1.006	-1.098
CCcont	0.444	0.996
DS01	0.238	1.483
DS02	-0.375	1.279
DS04	0.125	0.817
DS0c	0.644	1.381
GP01	0.682	0.817
GP02	0.178	0.135
GP0c	0.192	1.366
NOD	-0.218	-0.389
NZO	0.103	-2.092
PWK	0.503	-1.171
H37Rv_KO_CtpC	1.407	0.744
H37Rv_KO_CtpD	0.299	1.382
H37Rv_KO_Rv1272	1.469	1.874
H37Rv_KO_SugABC	1.395	0.592
H37Rv_KO_MbtN	0.21	0.841
Trans05	0.92	1.403
macrophage_unactivated	1.111	0.357
IL1	0.676	1.011
Rapamycin	0.246	1.157
Tcell	0.668	0.414
GMCSF	0.784	1.167
IFNab	0.828	1.067
IFNg	1.053	0.959
IFNg_GMCSF1	0.49	0.811
Rv1432_day32	-0.117	-0.395
Rv1565c_day32	-0.542	-0.073
secA2_input	0.509	0.41
delta_Rv3594	-0.24	-0.509
delta_Rv3717	0.305	-0.24
delta_Rv3811	-0.214	-0.47
delta_Rv0954	-0.669	-0.408
PonA1	-0.777	-0.955
EccD1_KO	-0.51	0.934
EspI_KO	-1.072	0.87
PE35_KO	0.184	1.035
PPE68_KO	0.422	1.238
glycerol2	0.581	2.092
lignocerate	1.132	0.997
oleate	1.466	0.084
phosphatidylcholine	0.753	1.793
acetate	0.775	0.424
glucAc	0.0	0.253
Rv0950ko	-0.172	-0.015
Rv1096ko	0.066	-0.368
Rv3684ko	0.0	-0.095
delta_otsA_trehalose	-0.184	0.69