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 Rv3787c/-:
Show top 50 genes. Show bottom 10 genes with LOWEST correlation.

Most correlated genes.

update plot	correlation	link to info on gene
Rv2443/dctA	(cc=0.4697)	info on Rv2443/dctA
Rv3199c/nudC	(cc=0.4667)	info on Rv3199c/nudC
Rv2918c/glnD	(cc=0.4611)	info on Rv2918c/glnD
Rv2718c/nrdR	(cc=0.4599)	info on Rv2718c/nrdR
Rv0074/-	(cc=0.4534)	info on Rv0074/-
Rv0726c/-	(cc=0.4412)	info on Rv0726c/-
Rv0255c/cobQ1	(cc=0.4404)	info on Rv0255c/cobQ1
Rv3857c/-	(cc=0.4378)	info on Rv3857c/-
Rv3711c/dnaQ	(cc=0.4347)	info on Rv3711c/dnaQ
Rv3425/PPE57	(cc=0.4225)	info on Rv3425/PPE57

Correlation of Rv3787c/- with Rv2443/dctA

Normalized LFCs for Rv3787c/-:
(description and provenance of datasets)

Comparison of LFCs between selected condtions.

condition	Rv3787c/-	Rv2443/dctA
Fe_supp_jason_reseq	-0.745	-0.074
low_pH_jason_reseq	-1.111	-1.052
NO_jason_reseq	-0.827	-0.108
B6_jason_reseq	-0.546	-0.548
MHCII_jason_reseq	-0.436	-0.268
Isoniazid02	-0.49	-0.426
Rifampicin4	-0.225	0.049
Ethambutol3	-0.063	-0.383
Meropenem3	0.018	0.152
Vancomycin16	-0.098	-0.501
Rv2680_day32	-0.204	0.053
H37Rv_KO_MarP	0.577	-0.121
hypoxia_3wks	0.108	-0.068
hypoxia_6wks	-0.117	0.267
glycerol	0.018	-0.601
cholesterol	-0.366	0.37
AJ	0.624	0.977
Bibs02	-0.462	0.424
Bibs02c	0.832	-0.238
BL6	-0.033	0.607
BL6a	0.181	0.026
BXD01	-0.155	0.443
BXD010	-0.411	0.305
BXD011	-0.133	0.372
BXD03	0.313	0.386
BXD04	0.295	0.409
BXD05	-1.01	0.023
BXD06	0.017	0.535
BXD07	-0.388	0.444
BXD08	-0.567	0.468
BXD09	-0.056	0.321
CAST	0.541	0.469
CCcont	-0.705	-0.236
DS01	0.666	0.224
DS02	0.164	0.224
DS04	0.443	0.707
DS0c	0.181	0.127
GP01	-0.61	0.029
GP02	-0.111	1.221
GP0c	0.128	-0.023
NOD	-0.059	0.926
NZO	0.068	0.433
PWK	0.321	1.698
H37Rv_KO_CtpC	0.18	0.021
H37Rv_KO_CtpD	1.002	0.851
H37Rv_KO_Rv1272	-0.049	0.262
H37Rv_KO_SugABC	0.796	0.711
H37Rv_KO_MbtN	0.172	0.026
Trans05	-0.451	-0.081
macrophage_unactivated	-0.631	0.347
IL1	-0.077	-0.492
Rapamycin	0.193	-0.488
Tcell	-0.127	-0.14
GMCSF	-0.193	0.127
IFNab	-0.493	-0.166
IFNg	-0.016	0.556
IFNg_GMCSF1	1.279	0.892
Rv1432_day32	0.531	0.262
Rv1565c_day32	-1.251	0.889
secA2_input	0.376	-0.728
delta_Rv3594	-0.266	-0.486
delta_Rv3717	-0.584	-0.79
delta_Rv3811	-0.355	-0.431
delta_Rv0954	-0.075	0.481
PonA1	0.106	0.369
EccD1_KO	-1.125	-0.332
EspI_KO	-0.904	-0.599
PE35_KO	-0.785	-0.551
PPE68_KO	-1.094	-0.787
glycerol2	-0.251	0.067
lignocerate	-0.325	-0.03
oleate	0.15	0.492
phosphatidylcholine	-0.315	0.242
acetate	-0.221	-0.258
glucAc	-0.88	-0.762
Rv0950ko	-0.416	-0.25
Rv1096ko	-0.528	-0.835
Rv3684ko	-0.848	-0.698
delta_otsA_trehalose	0.975	0.483