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 Rv0861c/ercc3:

update plot	correlation	link to info on gene
Rv1324/-	(cc=0.5465)	info on Rv1324/-
Rv2169c/-	(cc=0.5449)	info on Rv2169c/-
Rv1638/uvrA	(cc=0.5351)	info on Rv1638/uvrA
Rv2518c/ldtB	(cc=0.5333)	info on Rv2518c/ldtB
Rv2535c/pepQ	(cc=0.51)	info on Rv2535c/pepQ
Rv2179c/-	(cc=0.5092)	info on Rv2179c/-
Rv1432/-	(cc=0.5023)	info on Rv1432/-
Rv0150c/-	(cc=0.4831)	info on Rv0150c/-
Rv2700/-	(cc=0.4696)	info on Rv2700/-
Rv1298/rpmE	(cc=0.4657)	info on Rv1298/rpmE

Correlation of Rv0861c/ercc3 with Rv2179c/-

Normalized LFCs for Rv0861c/ercc3:
(description and provenance of datasets)

	Rv0861c/ercc3	Rv2179c/-
Fe_supp_jason_reseq	0.423	0.655
low_pH_jason_reseq	-0.055	1.233
NO_jason_reseq	0.633	-1.536
B6_jason_reseq	-1.039	-0.496
MHCII_jason_reseq	1.426	-0.572
Isoniazid02	0.419	-1.026
Rifampicin4	-0.125	-4.473
Ethambutol3	0.551	1.423
Meropenem3	-0.386	0.338
Vancomycin16	0.04	-4.247
Rv2680_day32	0.922	-0.249
H37Rv_KO_MarP	0.025	-4.589
hypoxia_3wks	-0.471	-6.0
hypoxia_6wks	-0.658	-5.055
glycerol	0.891	1.972
cholesterol	0.663	-0.145
AJ	0.392	-0.232
Bibs02	-1.142	-0.183
Bibs02c	-0.056	-0.209
BL6	0.343	3.134
BL6a	0.544	0.776
BXD01	0.458	2.751
BXD010	0.73	1.471
BXD011	0.819	0.795
BXD03	0.035	1.509
BXD04	0.124	3.583
BXD05	0.846	1.21
BXD06	0.283	3.86
BXD07	0.68	1.245
BXD08	1.202	3.613
BXD09	0.904	1.657
CAST	0.389	-0.23
CCcont	0.607	3.902
DS01	0.695	-0.236
DS02	0.414	-0.217
DS04	0.492	2.459
DS0c	0.46	-0.217
GP01	-0.026	0.508
GP02	1.011	0.269
GP0c	0.659	0.119
NOD	-0.452	1.282
NZO	0.15	0.0
PWK	0.689	-0.196
H37Rv_KO_CtpC	1.259	0.835
H37Rv_KO_CtpD	1.029	0.651
H37Rv_KO_Rv1272	0.804	0.725
H37Rv_KO_SugABC	0.678	2.752
H37Rv_KO_MbtN	1.438	4.067
Trans05	0.894	0.947
macrophage_unactivated	1.111	3.156
IL1	0.899	0.451
Rapamycin	0.531	1.63
Tcell	1.069	4.989
GMCSF	0.734	-1.143
IFNab	0.269	0.157
IFNg	0.676	-1.157
IFNg_GMCSF1	1.471	0.163
Rv1432_day32	-0.42	-0.763
Rv1565c_day32	1.461	0.0
secA2_input	0.448	-1.154
delta_Rv3594	1.054	1.427
delta_Rv3717	1.516	2.503
delta_Rv3811	1.304	1.463
delta_Rv0954	1.027	-2.271
PonA1	-0.338	-4.067
EccD1_KO	0.73	-2.513
EspI_KO	0.248	-1.095
PE35_KO	1.706	0.449
PPE68_KO	1.609	1.001
glycerol2	-0.64	0.352
lignocerate	-0.257	-3.383
oleate	-0.906	-5.721
phosphatidylcholine	-0.857	-3.891
acetate	-0.49	-0.981
glucAc	-0.328	-0.931
Rv0950ko	-1.167	-3.618
Rv1096ko	-0.908	-0.992
Rv3684ko	-0.527	-0.508
delta_otsA_trehalose	0.122	0.234