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 Rv2715/-:

update plot	correlation	link to info on gene
Rv2394/ggtB	(cc=0.6425)	info on Rv2394/ggtB
Rv0338c/-	(cc=0.5414)	info on Rv0338c/-
Rv2268c/cyp128	(cc=0.4909)	info on Rv2268c/cyp128
Rv2189c/-	(cc=0.4775)	info on Rv2189c/-
Rv0373c/-	(cc=0.4709)	info on Rv0373c/-
Rv1317c/alkA	(cc=0.4611)	info on Rv1317c/alkA
Rv3730c/-	(cc=0.4507)	info on Rv3730c/-
Rv0069c/sdaA	(cc=0.4477)	info on Rv0069c/sdaA
Rv2962c/-	(cc=0.437)	info on Rv2962c/-
Rv0797/-	(cc=0.4327)	info on Rv0797/-

Correlation of Rv2715/- with Rv2268c/cyp128

Normalized LFCs for Rv2715/-:
(description and provenance of datasets)

	Rv2715/-	Rv2268c/cyp128
Fe_supp_jason_reseq	-0.508	-0.906
low_pH_jason_reseq	0.796	-0.196
NO_jason_reseq	-0.646	-0.714
B6_jason_reseq	-0.542	-0.834
MHCII_jason_reseq	0.346	-1.068
Isoniazid02	1.224	-0.105
Rifampicin4	-0.504	-0.298
Ethambutol3	2.932	-0.134
Meropenem3	2.498	0.875
Vancomycin16	0.0	0.0
Rv2680_day32	-0.73	-0.874
H37Rv_KO_MarP	0.223	-0.11
hypoxia_3wks	-0.116	-0.518
hypoxia_6wks	0.175	-0.161
glycerol	-0.471	1.434
cholesterol	4.799	6.0
AJ	-0.024	0.632
Bibs02	-0.223	0.792
Bibs02c	1.516	1.299
BL6	0.26	1.26
BL6a	1.24	0.623
BXD01	0.314	0.489
BXD010	1.166	0.0
BXD011	0.642	0.29
BXD03	0.349	1.271
BXD04	0.809	-0.408
BXD05	0.369	0.814
BXD06	0.366	0.334
BXD07	0.357	0.377
BXD08	0.448	0.648
BXD09	0.788	0.527
CAST	-0.28	1.039
CCcont	0.348	0.082
DS01	0.429	0.065
DS02	0.132	1.022
DS04	0.682	-1.248
DS0c	0.046	1.095
GP01	0.804	-0.802
GP02	0.516	1.79
GP0c	0.387	-0.836
NOD	1.787	1.595
NZO	-0.964	1.329
PWK	0.158	0.108
H37Rv_KO_CtpC	0.607	-0.473
H37Rv_KO_CtpD	0.185	1.684
H37Rv_KO_Rv1272	0.558	1.022
H37Rv_KO_SugABC	0.898	1.209
H37Rv_KO_MbtN	1.101	0.933
Trans05	1.278	0.982
macrophage_unactivated	0.3	-0.354
IL1	-0.065	0.308
Rapamycin	0.353	-0.718
Tcell	0.176	0.45
GMCSF	-0.148	0.774
IFNab	-0.133	-0.707
IFNg	0.644	-0.299
IFNg_GMCSF1	-0.358	-0.735
Rv1432_day32	-0.499	0.287
Rv1565c_day32	-0.655	0.602
secA2_input	-0.11	-0.146
delta_Rv3594	0.728	0.912
delta_Rv3717	0.151	0.0
delta_Rv3811	1.169	0.049
delta_Rv0954	0.783	-0.23
PonA1	0.386	-0.039
EccD1_KO	1.095	-1.059
EspI_KO	0.95	-0.168
PE35_KO	1.476	0.904
PPE68_KO	0.784	0.442
glycerol2	-0.476	0.144
lignocerate	0.102	-0.346
oleate	-0.216	-0.483
phosphatidylcholine	0.0	-0.132
acetate	0.206	-0.183
glucAc	0.481	-0.565
Rv0950ko	-0.109	-0.808
Rv1096ko	-0.145	-0.808
Rv3684ko	-0.318	-0.783
delta_otsA_trehalose	0.879	-0.838