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 Rv3540c/ltp2:
Show top 50 genes. Show bottom 10 genes with LOWEST correlation.

Most correlated genes.

update plot	correlation	link to info on gene
Rv3551/-	(cc=0.7764)	info on Rv3551/-
Rv3544c/fadE28	(cc=0.7616)	info on Rv3544c/fadE28
Rv3870/eccCa1	(cc=0.7568)	info on Rv3870/eccCa1
Rv3883c/mycP1	(cc=0.7539)	info on Rv3883c/mycP1
Rv3542c/-	(cc=0.7521)	info on Rv3542c/-
Rv3869/eccB1	(cc=0.7491)	info on Rv3869/eccB1
Rv3535c/hsaG	(cc=0.7415)	info on Rv3535c/hsaG
Rv3550/echA20	(cc=0.7398)	info on Rv3550/echA20
Rv3553/-	(cc=0.7288)	info on Rv3553/-
Rv3502c/-	(cc=0.7287)	info on Rv3502c/-

Correlation of Rv3540c/ltp2 with Rv3551/-

Normalized LFCs for Rv3540c/ltp2:
(description and provenance of datasets)

Comparison of LFCs between selected condtions.

condition	Rv3540c/ltp2	Rv3551/-
Fe_supp_jason_reseq	-0.218	0.737
low_pH_jason_reseq	0.979	-0.647
NO_jason_reseq	-0.176	-0.601
B6_jason_reseq	-2.219	-1.96
MHCII_jason_reseq	-1.719	-1.726
Isoniazid02	2.103	-0.842
Rifampicin4	-0.171	-0.165
Ethambutol3	2.831	-1.515
Meropenem3	-0.236	0.734
Vancomycin16	-0.618	-1.008
Rv2680_day32	0.0	-1.788
H37Rv_KO_MarP	-0.169	0.246
hypoxia_3wks	-0.132	0.08
hypoxia_6wks	-0.069	-0.693
glycerol	1.065	1.148
cholesterol	-1.761	-3.657
AJ	-2.82	-5.857
Bibs02	-2.223	-4.616
Bibs02c	-1.97	-5.282
BL6	-0.752	-2.92
BL6a	-2.03	-5.001
BXD01	-1.227	-3.288
BXD010	-1.107	-2.306
BXD011	-0.042	-2.59
BXD03	0.417	-3.28
BXD04	-1.38	-2.999
BXD05	-1.38	-3.029
BXD06	-1.623	-3.37
BXD07	-1.197	-3.496
BXD08	-1.363	-3.226
BXD09	-1.44	-3.408
CAST	-2.571	-4.838
CCcont	0.757	-0.733
DS01	-2.871	-5.963
DS02	-2.644	-5.49
DS04	-1.989	-4.367
DS0c	-2.637	-5.476
GP01	-1.102	-2.304
GP02	-0.929	-1.942
GP0c	0.785	-1.016
NOD	-1.351	-1.847
NZO	-2.425	-4.838
PWK	-2.384	-4.757
H37Rv_KO_CtpC	-1.813	-3.94
H37Rv_KO_CtpD	-1.095	-2.576
H37Rv_KO_Rv1272	-1.022	-3.56
H37Rv_KO_SugABC	-1.106	-1.783
H37Rv_KO_MbtN	-1.056	-1.855
Trans05	-0.512	-3.299
macrophage_unactivated	-0.83	0.66
IL1	-0.451	-1.605
Rapamycin	0.0	-1.093
Tcell	-3.584	-2.209
GMCSF	0.246	0.752
IFNab	2.316	2.283
IFNg	1.013	-0.249
IFNg_GMCSF1	-1.405	-0.606
Rv1432_day32	-0.18	-3.863
Rv1565c_day32	-0.766	-3.884
secA2_input	1.249	-0.54
delta_Rv3594	-0.225	-0.26
delta_Rv3717	0.37	0.191
delta_Rv3811	0.437	0.556
delta_Rv0954	0.652	1.149
PonA1	0.693	0.384
EccD1_KO	0.635	1.246
EspI_KO	0.918	0.539
PE35_KO	0.292	1.105
PPE68_KO	0.32	1.139
glycerol2	1.292	0.289
lignocerate	1.628	0.785
oleate	-1.117	-0.537
phosphatidylcholine	0.854	-0.106
acetate	2.068	2.234
glucAc	2.286	1.052
Rv0950ko	0.093	1.903
Rv1096ko	1.3	0.329
Rv3684ko	0.845	0.092
delta_otsA_trehalose	0.327	0.325