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 Rv3066/-:
Show top 50 genes. Show bottom 10 genes with LOWEST correlation.

Most correlated genes.

update plot	correlation	link to info on gene
Rv0113/gmhA	(cc=0.4169)	info on Rv0113/gmhA
Rv0243/fadA2	(cc=0.4069)	info on Rv0243/fadA2
Rv3638/-	(cc=0.4034)	info on Rv3638/-
Rv2765/-	(cc=0.4021)	info on Rv2765/-
Rv0659c/mazF2	(cc=0.4014)	info on Rv0659c/mazF2
Rv0233/nrdB	(cc=0.4013)	info on Rv0233/nrdB
Rv1349/irtB	(cc=0.3909)	info on Rv1349/irtB
Rv1881c/lppE	(cc=0.3874)	info on Rv1881c/lppE
Rv3328c/sigJ	(cc=0.3849)	info on Rv3328c/sigJ
Rv0307c/-	(cc=0.3847)	info on Rv0307c/-

Correlation of Rv3066/- with Rv0113/gmhA

Normalized LFCs for Rv3066/-:
(description and provenance of datasets)

Comparison of LFCs between selected condtions.

condition	Rv3066/-	Rv0113/gmhA
Fe_supp_jason_reseq	3.647	2.595
low_pH_jason_reseq	0.371	-0.831
NO_jason_reseq	-2.625	-1.536
B6_jason_reseq	0.736	3.067
MHCII_jason_reseq	2.556	2.446
Isoniazid02	-0.626	1.801
Rifampicin4	1.01	0.1
Ethambutol3	-0.488	0.327
Meropenem3	-0.137	-0.341
Vancomycin16	0.438	-0.098
Rv2680_day32	1.042	0.0
H37Rv_KO_MarP	-0.206	0.754
hypoxia_3wks	2.46	-0.415
hypoxia_6wks	-0.34	-0.708
glycerol	-1.954	0.398
cholesterol	-2.77	-0.353
AJ	1.857	0.874
Bibs02	0.105	2.099
Bibs02c	0.179	2.536
BL6	-0.6	-0.982
BL6a	-0.142	1.936
BXD01	-0.625	-0.079
BXD010	-0.36	0.273
BXD011	-0.948	0.097
BXD03	-1.062	-1.526
BXD04	-1.024	-0.5
BXD05	-0.378	-2.089
BXD06	-0.941	0.051
BXD07	-0.407	0.227
BXD08	-0.013	-0.053
BXD09	-0.548	-0.886
CAST	-0.045	1.552
CCcont	0.511	-0.255
DS01	2.038	2.712
DS02	1.82	2.039
DS04	0.922	2.791
DS0c	1.416	2.918
GP01	0.084	-1.236
GP02	0.539	0.899
GP0c	-0.163	0.416
NOD	0.291	1.671
NZO	0.095	-0.207
PWK	-0.29	0.6
H37Rv_KO_CtpC	0.167	-0.065
H37Rv_KO_CtpD	0.73	1.187
H37Rv_KO_Rv1272	-0.471	-0.415
H37Rv_KO_SugABC	0.171	1.38
H37Rv_KO_MbtN	-0.788	1.197
Trans05	0.062	-0.689
macrophage_unactivated	0.799	0.12
IL1	-1.261	-0.489
Rapamycin	-0.826	-1.396
Tcell	0.0	-0.261
GMCSF	0.198	0.573
IFNab	0.227	-0.916
IFNg	-0.126	-0.559
IFNg_GMCSF1	-0.789	0.682
Rv1432_day32	0.48	2.356
Rv1565c_day32	0.649	-0.415
secA2_input	-1.414	-0.188
delta_Rv3594	0.216	3.223
delta_Rv3717	-0.731	1.258
delta_Rv3811	-1.109	0.813
delta_Rv0954	-0.057	1.95
PonA1	-0.01	2.546
EccD1_KO	-0.622	-1.5
EspI_KO	-0.054	-2.524
PE35_KO	0.487	-1.097
PPE68_KO	-0.09	-1.328
glycerol2	0.0	0.311
lignocerate	-0.591	0.868
oleate	-0.493	0.588
phosphatidylcholine	-0.487	0.496
acetate	-0.579	0.836
glucAc	0.375	0.971
Rv0950ko	-0.558	1.423
Rv1096ko	-0.093	-0.142
Rv3684ko	-0.684	0.151
delta_otsA_trehalose	-0.785	0.305