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 Rv3394c/-:

update plot	correlation	link to info on gene
Rv3511/PE_PGRS55	(cc=0.5008)	info on Rv3511/PE_PGRS55
Rv3514/PE_PGRS57	(cc=0.4562)	info on Rv3514/PE_PGRS57
Rv3508/PE_PGRS54	(cc=0.4517)	info on Rv3508/PE_PGRS54
Rv2853/PE_PGRS48	(cc=0.4274)	info on Rv2853/PE_PGRS48
Rv2431c/PE25	(cc=0.405)	info on Rv2431c/PE25
Rv0834c/PE_PGRS14	(cc=0.4013)	info on Rv0834c/PE_PGRS14
Rv0142/-	(cc=0.3995)	info on Rv0142/-
Rv3299c/atsB	(cc=0.399)	info on Rv3299c/atsB
Rv0858c/dapC	(cc=0.3974)	info on Rv0858c/dapC
Rv3470c/ilvB2	(cc=0.3907)	info on Rv3470c/ilvB2

Correlation of Rv3394c/- with Rv0142/-

Normalized LFCs for Rv3394c/-:
(description and provenance of datasets)

	Rv3394c/-	Rv0142/-
Fe_supp_jason_reseq	-0.829	-1.579
low_pH_jason_reseq	1.228	-1.369
NO_jason_reseq	0.591	-0.612
B6_jason_reseq	-1.269	-3.671
MHCII_jason_reseq	-0.58	-2.222
Isoniazid02	-0.339	-0.195
Rifampicin4	0.72	0.531
Ethambutol3	-0.197	0.225
Meropenem3	0.207	0.055
Vancomycin16	0.0	-0.255
Rv2680_day32	-0.422	-0.971
H37Rv_KO_MarP	0.289	0.656
hypoxia_3wks	0.439	-0.845
hypoxia_6wks	-0.048	-1.034
glycerol	2.058	1.807
cholesterol	1.696	0.295
AJ	1.627	0.761
Bibs02	0.0	0.513
Bibs02c	0.756	0.964
BL6	0.16	0.0
BL6a	0.443	1.386
BXD01	0.029	1.251
BXD010	0.4	-0.493
BXD011	0.137	1.031
BXD03	0.399	0.521
BXD04	0.486	0.954
BXD05	0.373	0.897
BXD06	0.417	0.438
BXD07	0.232	0.227
BXD08	1.2	0.731
BXD09	0.39	-0.445
CAST	0.385	1.178
CCcont	0.677	0.223
DS01	0.777	0.45
DS02	0.364	0.978
DS04	1.147	1.64
DS0c	-0.823	0.442
GP01	1.305	1.062
GP02	1.89	1.449
GP0c	0.769	1.746
NOD	-0.158	-0.187
NZO	0.446	1.363
PWK	0.0	0.983
H37Rv_KO_CtpC	0.587	0.831
H37Rv_KO_CtpD	0.351	0.918
H37Rv_KO_Rv1272	1.115	-1.597
H37Rv_KO_SugABC	0.659	0.977
H37Rv_KO_MbtN	-0.024	-0.445
Trans05	1.567	0.504
macrophage_unactivated	-0.114	0.947
IL1	0.727	1.053
Rapamycin	-0.055	0.249
Tcell	-0.554	0.554
GMCSF	0.317	0.908
IFNab	-0.109	1.327
IFNg	0.406	-1.871
IFNg_GMCSF1	1.09	0.572
Rv1432_day32	1.112	1.494
Rv1565c_day32	1.887	0.218
secA2_input	0.269	-0.139
delta_Rv3594	-0.078	0.982
delta_Rv3717	0.062	0.505
delta_Rv3811	0.073	0.338
delta_Rv0954	0.124	0.966
PonA1	0.329	1.444
EccD1_KO	0.753	-0.875
EspI_KO	-0.322	-2.892
PE35_KO	-0.137	-2.161
PPE68_KO	0.099	-2.16
glycerol2	-0.059	-0.094
lignocerate	0.499	-0.412
oleate	0.274	0.449
phosphatidylcholine	0.296	-0.275
acetate	0.733	-0.482
glucAc	0.307	0.027
Rv0950ko	0.1	-0.256
Rv1096ko	0.473	0.329
Rv3684ko	1.52	-0.422
delta_otsA_trehalose	-0.045	-1.05