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 Rv3665c/dppB:

update plot	correlation	link to info on gene
Rv3776/-	(cc=0.4675)	info on Rv3776/-
Rv1944c/-	(cc=0.4409)	info on Rv1944c/-
Rv3813c/-	(cc=0.4353)	info on Rv3813c/-
Rv2665/-	(cc=0.4068)	info on Rv2665/-
Rv2804c/-	(cc=0.4004)	info on Rv2804c/-
Rv1845c/blaR	(cc=0.397)	info on Rv1845c/blaR
Rv3481c/-	(cc=0.3932)	info on Rv3481c/-
Rv1100/-	(cc=0.3866)	info on Rv1100/-
Rv2206/-	(cc=0.382)	info on Rv2206/-
Rv1020/mfd	(cc=0.3785)	info on Rv1020/mfd

Correlation of Rv3665c/dppB with Rv2665/-

Normalized LFCs for Rv3665c/dppB:
(description and provenance of datasets)

	Rv3665c/dppB	Rv2665/-
Fe_supp_jason_reseq	-0.365	-0.783
low_pH_jason_reseq	2.515	-0.597
NO_jason_reseq	-1.982	-0.473
B6_jason_reseq	-2.162	-1.301
MHCII_jason_reseq	-1.4	-0.097
Isoniazid02	-0.506	-0.368
Rifampicin4	0.165	0.487
Ethambutol3	1.667	0.272
Meropenem3	-0.689	1.252
Vancomycin16	-0.111	0.525
Rv2680_day32	0.573	1.145
H37Rv_KO_MarP	-0.272	0.799
hypoxia_3wks	0.327	0.415
hypoxia_6wks	-0.478	0.238
glycerol	0.654	-0.039
cholesterol	0.854	0.147
AJ	0.751	1.331
Bibs02	1.142	0.727
Bibs02c	0.474	0.94
BL6	0.906	1.076
BL6a	0.062	0.914
BXD01	0.0	0.695
BXD010	0.8	0.818
BXD011	0.078	0.695
BXD03	-0.135	1.396
BXD04	-0.524	0.675
BXD05	-0.636	1.803
BXD06	0.233	0.992
BXD07	0.279	0.913
BXD08	-0.442	1.145
BXD09	0.488	1.296
CAST	1.185	0.692
CCcont	0.585	0.643
DS01	0.975	0.38
DS02	0.321	0.589
DS04	1.744	1.047
DS0c	1.199	0.905
GP01	0.699	0.468
GP02	-0.175	-0.328
GP0c	0.834	0.293
NOD	0.205	0.343
NZO	-0.663	1.783
PWK	0.0	0.755
H37Rv_KO_CtpC	1.949	1.472
H37Rv_KO_CtpD	-0.316	2.181
H37Rv_KO_Rv1272	-1.067	-0.174
H37Rv_KO_SugABC	1.302	0.494
H37Rv_KO_MbtN	-0.715	-0.01
Trans05	-1.5	0.038
macrophage_unactivated	-0.593	0.249
IL1	-0.439	-0.721
Rapamycin	-1.099	-1.157
Tcell	0.332	-0.978
GMCSF	-0.391	-0.317
IFNab	0.502	-0.453
IFNg	-0.502	-0.203
IFNg_GMCSF1	-1.266	-1.442
Rv1432_day32	0.0	-0.139
Rv1565c_day32	0.646	0.453
secA2_input	-0.167	0.268
delta_Rv3594	-1.071	-0.249
delta_Rv3717	-1.33	-0.274
delta_Rv3811	-0.674	-0.98
delta_Rv0954	-0.111	-0.142
PonA1	-0.316	0.817
EccD1_KO	-1.168	-0.036
EspI_KO	0.493	-0.665
PE35_KO	-0.236	-0.755
PPE68_KO	-0.928	0.202
glycerol2	0.261	-0.353
lignocerate	0.06	-0.069
oleate	-0.345	0.187
phosphatidylcholine	0.492	-0.161
acetate	-0.216	0.076
glucAc	-0.554	-0.379
Rv0950ko	-0.178	0.199
Rv1096ko	0.172	0.329
Rv3684ko	-0.498	-0.111
delta_otsA_trehalose	-2.907	-1.481