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 Rv1710/scpB:

update plot	correlation	link to info on gene
Rv1167c/-	(cc=0.5279)	info on Rv1167c/-
Rv1575/-	(cc=0.5044)	info on Rv1575/-
Rv1633/uvrB	(cc=0.5043)	info on Rv1633/uvrB
Rv1709/scpA	(cc=0.5023)	info on Rv1709/scpA
Rv3161c/-	(cc=0.4701)	info on Rv3161c/-
Rv3232c/ppk2	(cc=0.4674)	info on Rv3232c/ppk2
Rv3108/-	(cc=0.4659)	info on Rv3108/-
Rv1116/-	(cc=0.4644)	info on Rv1116/-
Rv1456c/-	(cc=0.4584)	info on Rv1456c/-
Rv3720/-	(cc=0.4577)	info on Rv3720/-

Correlation of Rv1710/scpB with Rv3161c/-

Normalized LFCs for Rv1710/scpB:
(description and provenance of datasets)

	Rv1710/scpB	Rv3161c/-
Fe_supp_jason_reseq	-0.546	0.153
low_pH_jason_reseq	-0.649	0.293
NO_jason_reseq	1.796	0.11
B6_jason_reseq	-0.741	-0.414
MHCII_jason_reseq	-0.785	-0.538
Isoniazid02	-1.228	-0.509
Rifampicin4	0.097	-0.03
Ethambutol3	-0.483	-0.409
Meropenem3	-0.722	-0.068
Vancomycin16	-0.929	0.088
Rv2680_day32	-1.19	-0.422
H37Rv_KO_MarP	-1.067	0.454
hypoxia_3wks	-1.284	-0.052
hypoxia_6wks	-1.927	-0.338
glycerol	0.945	1.001
cholesterol	0.947	0.628
AJ	-1.119	0.244
Bibs02	-0.578	0.695
Bibs02c	0.756	0.653
BL6	1.783	0.376
BL6a	0.748	0.798
BXD01	0.683	0.859
BXD010	0.822	1.108
BXD011	0.163	0.84
BXD03	1.652	1.053
BXD04	0.579	0.896
BXD05	1.147	0.864
BXD06	0.921	0.369
BXD07	0.872	0.332
BXD08	0.804	0.748
BXD09	0.794	0.319
CAST	-0.591	0.242
CCcont	-0.34	0.648
DS01	0.737	0.625
DS02	0.0	-0.142
DS04	-0.498	0.696
DS0c	0.853	0.198
GP01	-0.17	0.761
GP02	0.0	0.985
GP0c	-0.091	1.527
NOD	-1.432	0.138
NZO	-0.757	0.527
PWK	-1.708	0.612
H37Rv_KO_CtpC	1.803	1.504
H37Rv_KO_CtpD	0.187	1.284
H37Rv_KO_Rv1272	0.208	1.574
H37Rv_KO_SugABC	-0.225	1.01
H37Rv_KO_MbtN	0.686	1.145
Trans05	2.57	1.872
macrophage_unactivated	-0.082	0.799
IL1	0.359	-0.564
Rapamycin	0.227	0.178
Tcell	0.319	0.127
GMCSF	0.319	2.587
IFNab	0.895	0.345
IFNg	-1.366	-0.163
IFNg_GMCSF1	0.93	0.635
Rv1432_day32	-1.026	-0.66
Rv1565c_day32	0.739	0.85
secA2_input	0.537	0.219
delta_Rv3594	0.353	0.838
delta_Rv3717	0.311	0.853
delta_Rv3811	-0.375	0.779
delta_Rv0954	-1.081	0.452
PonA1	0.044	0.77
EccD1_KO	1.783	0.227
EspI_KO	1.395	0.998
PE35_KO	0.805	0.543
PPE68_KO	1.328	0.902
glycerol2	-0.886	0.275
lignocerate	-0.309	0.332
oleate	-0.948	0.713
phosphatidylcholine	-0.279	0.664
acetate	-1.051	-0.246
glucAc	-0.617	-0.514
Rv0950ko	0.06	-0.582
Rv1096ko	0.181	-0.413
Rv3684ko	-0.275	-0.033
delta_otsA_trehalose	0.378	0.371