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 Rv1456c/-

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

	Rv1710/scpB	Rv1456c/-
Fe_supp_jason_reseq	-0.546	1.266
low_pH_jason_reseq	-0.649	-0.261
NO_jason_reseq	1.796	-0.41
B6_jason_reseq	-0.741	-1.886
MHCII_jason_reseq	-0.785	-1.171
Isoniazid02	-1.228	0.0
Rifampicin4	0.097	-0.523
Ethambutol3	-0.483	-0.09
Meropenem3	-0.722	-0.231
Vancomycin16	-0.929	-0.196
Rv2680_day32	-1.19	0.347
H37Rv_KO_MarP	-1.067	-0.586
hypoxia_3wks	-1.284	1.049
hypoxia_6wks	-1.927	0.422
glycerol	0.945	-0.136
cholesterol	0.947	0.0
AJ	-1.119	0.771
Bibs02	-0.578	-0.397
Bibs02c	0.756	-0.82
BL6	1.783	0.154
BL6a	0.748	0.462
BXD01	0.683	-0.182
BXD010	0.822	2.068
BXD011	0.163	0.08
BXD03	1.652	0.888
BXD04	0.579	0.222
BXD05	1.147	0.787
BXD06	0.921	1.131
BXD07	0.872	1.003
BXD08	0.804	0.31
BXD09	0.794	0.089
CAST	-0.591	-1.131
CCcont	-0.34	0.348
DS01	0.737	-0.159
DS02	0.0	-1.068
DS04	-0.498	0.736
DS0c	0.853	0.137
GP01	-0.17	-0.067
GP02	0.0	-0.116
GP0c	-0.091	1.884
NOD	-1.432	-0.675
NZO	-0.757	-0.279
PWK	-1.708	-0.769
H37Rv_KO_CtpC	1.803	1.968
H37Rv_KO_CtpD	0.187	1.508
H37Rv_KO_Rv1272	0.208	1.524
H37Rv_KO_SugABC	-0.225	-0.388
H37Rv_KO_MbtN	0.686	2.974
Trans05	2.57	1.914
macrophage_unactivated	-0.082	-0.164
IL1	0.359	-0.154
Rapamycin	0.227	-0.16
Tcell	0.319	-0.531
GMCSF	0.319	2.131
IFNab	0.895	0.444
IFNg	-1.366	0.0
IFNg_GMCSF1	0.93	1.263
Rv1432_day32	-1.026	0.0
Rv1565c_day32	0.739	0.539
secA2_input	0.537	0.462
delta_Rv3594	0.353	0.389
delta_Rv3717	0.311	0.135
delta_Rv3811	-0.375	0.576
delta_Rv0954	-1.081	0.444
PonA1	0.044	1.764
EccD1_KO	1.783	2.276
EspI_KO	1.395	2.347
PE35_KO	0.805	1.811
PPE68_KO	1.328	2.102
glycerol2	-0.886	-0.193
lignocerate	-0.309	-0.673
oleate	-0.948	-0.301
phosphatidylcholine	-0.279	-0.193
acetate	-1.051	0.209
glucAc	-0.617	-0.785
Rv0950ko	0.06	0.552
Rv1096ko	0.181	-0.241
Rv3684ko	-0.275	-0.54
delta_otsA_trehalose	0.378	0.595