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 Rv3022A/PE29:

update plot	correlation	link to info on gene
Rv2543/lppA	(cc=0.5866)	info on Rv2543/lppA
Rv1396c/PE_PGRS25	(cc=0.548)	info on Rv1396c/PE_PGRS25
Rv0526/-	(cc=0.5258)	info on Rv0526/-
Rv2519/PE26	(cc=0.5243)	info on Rv2519/PE26
Rv1173/fbiC	(cc=0.5135)	info on Rv1173/fbiC
Rv2807/-	(cc=0.5131)	info on Rv2807/-
Rv1067c/PE_PGRS19	(cc=0.5123)	info on Rv1067c/PE_PGRS19
Rv1918c/PPE35	(cc=0.5079)	info on Rv1918c/PPE35
Rv3023c/-	(cc=0.5041)	info on Rv3023c/-
Rv1047/-	(cc=0.5)	info on Rv1047/-

Correlation of Rv3022A/PE29 with Rv2543/lppA

Normalized LFCs for Rv3022A/PE29:
(description and provenance of datasets)

	Rv3022A/PE29	Rv2543/lppA
Fe_supp_jason_reseq	0.275	0.341
low_pH_jason_reseq	-0.381	-0.425
NO_jason_reseq	-0.709	-0.071
B6_jason_reseq	-0.585	-0.306
MHCII_jason_reseq	-0.709	-0.109
Isoniazid02	0.994	0.646
Rifampicin4	0.967	0.455
Ethambutol3	0.434	0.298
Meropenem3	0.291	0.446
Vancomycin16	0.594	0.756
Rv2680_day32	-0.826	0.076
H37Rv_KO_MarP	0.165	0.251
hypoxia_3wks	0.347	0.148
hypoxia_6wks	-0.81	0.411
glycerol	0.73	0.392
cholesterol	1.146	-0.031
AJ	2.274	0.61
Bibs02	0.167	0.735
Bibs02c	0.893	0.311
BL6	0.569	-0.333
BL6a	0.641	0.948
BXD01	0.898	-0.177
BXD010	0.456	1.033
BXD011	0.286	0.247
BXD03	0.216	1.097
BXD04	0.063	0.039
BXD05	0.775	0.689
BXD06	0.593	0.917
BXD07	0.93	0.305
BXD08	0.28	0.316
BXD09	0.383	0.683
CAST	1.099	0.959
CCcont	1.022	-0.016
DS01	0.883	0.479
DS02	0.745	0.711
DS04	0.748	0.877
DS0c	-0.019	0.888
GP01	0.72	0.292
GP02	0.311	0.421
GP0c	0.208	0.818
NOD	0.919	0.626
NZO	-0.088	0.474
PWK	0.494	-0.416
H37Rv_KO_CtpC	1.553	2.045
H37Rv_KO_CtpD	1.287	2.271
H37Rv_KO_Rv1272	2.221	1.102
H37Rv_KO_SugABC	0.898	-0.954
H37Rv_KO_MbtN	0.687	1.301
Trans05	1.378	1.206
macrophage_unactivated	0.767	0.489
IL1	0.039	0.62
Rapamycin	0.264	0.476
Tcell	0.525	0.228
GMCSF	1.333	0.62
IFNab	0.768	-0.03
IFNg	0.083	0.214
IFNg_GMCSF1	0.289	0.544
Rv1432_day32	0.85	-0.763
Rv1565c_day32	2.139	0.583
secA2_input	0.182	-1.478
delta_Rv3594	0.34	0.546
delta_Rv3717	0.145	-0.573
delta_Rv3811	0.427	-0.553
delta_Rv0954	-0.225	0.01
PonA1	0.516	-0.429
EccD1_KO	0.947	-0.806
EspI_KO	1.178	0.67
PE35_KO	0.84	-0.158
PPE68_KO	0.579	-0.026
glycerol2	-1.302	-1.922
lignocerate	-0.961	-1.793
oleate	-1.032	-1.923
phosphatidylcholine	-0.819	-1.709
acetate	-1.248	-1.436
glucAc	-0.722	-1.04
Rv0950ko	0.555	0.507
Rv1096ko	-0.347	-0.769
Rv3684ko	-0.354	-0.943
delta_otsA_trehalose	-1.531	-0.209