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 Rv3738c/PPE66

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

	Rv2497c/bkdA	Rv3738c/PPE66
Fe_supp_jason_reseq	-0.297	-0.238
low_pH_jason_reseq	0.244	-0.192
NO_jason_reseq	0.36	-0.034
B6_jason_reseq	-1.575	-0.216
MHCII_jason_reseq	0.011	0.063
Isoniazid02	-1.077	-0.949
Rifampicin4	0.263	-0.014
Ethambutol3	-1.058	-0.585
Meropenem3	-0.461	-0.751
Vancomycin16	-1.035	-0.825
Rv2680_day32	-0.473	0.525
H37Rv_KO_MarP	-0.144	0.365
hypoxia_3wks	0.634	-0.363
hypoxia_6wks	-0.578	-0.716
glycerol	-1.842	-0.75
cholesterol	0.311	-0.871
AJ	-0.062	-0.491
Bibs02	0.432	0.042
Bibs02c	0.426	1.031
BL6	0.255	0.475
BL6a	0.666	0.947
BXD01	0.147	0.456
BXD010	0.491	0.395
BXD011	0.476	0.668
BXD03	-0.389	0.155
BXD04	-0.334	0.142
BXD05	0.528	0.452
BXD06	0.342	0.191
BXD07	0.641	0.205
BXD08	0.118	0.124
BXD09	0.732	0.225
CAST	-1.006	-0.087
CCcont	0.444	0.094
DS01	0.238	-0.044
DS02	-0.375	0.03
DS04	0.125	0.215
DS0c	0.644	0.148
GP01	0.682	0.298
GP02	0.178	1.222
GP0c	0.192	0.739
NOD	-0.218	0.182
NZO	0.103	-0.624
PWK	0.503	0.134
H37Rv_KO_CtpC	1.407	0.718
H37Rv_KO_CtpD	0.299	1.243
H37Rv_KO_Rv1272	1.469	0.297
H37Rv_KO_SugABC	1.395	0.756
H37Rv_KO_MbtN	0.21	0.763
Trans05	0.92	0.529
macrophage_unactivated	1.111	0.496
IL1	0.676	0.605
Rapamycin	0.246	0.178
Tcell	0.668	0.316
GMCSF	0.784	0.356
IFNab	0.828	0.018
IFNg	1.053	-0.128
IFNg_GMCSF1	0.49	-0.057
Rv1432_day32	-0.117	0.297
Rv1565c_day32	-0.542	-0.046
secA2_input	0.509	0.46
delta_Rv3594	-0.24	-0.488
delta_Rv3717	0.305	-0.881
delta_Rv3811	-0.214	-0.892
delta_Rv0954	-0.669	-0.198
PonA1	-0.777	-0.443
EccD1_KO	-0.51	-0.234
EspI_KO	-1.072	-0.359
PE35_KO	0.184	-0.327
PPE68_KO	0.422	-0.154
glycerol2	0.581	0.824
lignocerate	1.132	0.927
oleate	1.466	0.953
phosphatidylcholine	0.753	0.975
acetate	0.775	0.076
glucAc	0.0	0.269
Rv0950ko	-0.172	0.458
Rv1096ko	0.066	-0.377
Rv3684ko	0.0	-0.269
delta_otsA_trehalose	-0.184	1.259