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 Rv1066/-:

update plot	correlation	link to info on gene
Rv3892c/PPE69	(cc=0.5115)	info on Rv3892c/PPE69
Rv2601/speE	(cc=0.5104)	info on Rv2601/speE
Rv0481c/-	(cc=0.5008)	info on Rv0481c/-
Rv3297/nei	(cc=0.4936)	info on Rv3297/nei
Rv2340c/PE_PGRS39	(cc=0.4893)	info on Rv2340c/PE_PGRS39
Rv3471c/-	(cc=0.4834)	info on Rv3471c/-
Rv2114/-	(cc=0.4788)	info on Rv2114/-
Rv1840c/PE_PGRS34	(cc=0.4705)	info on Rv1840c/PE_PGRS34
Rv0621/-	(cc=0.4637)	info on Rv0621/-
Rv2125/-	(cc=0.4628)	info on Rv2125/-

Correlation of Rv1066/- with Rv2125/-

Normalized LFCs for Rv1066/-:
(description and provenance of datasets)

	Rv1066/-	Rv2125/-
Fe_supp_jason_reseq	-0.63	0.845
low_pH_jason_reseq	-0.383	-0.231
NO_jason_reseq	-1.859	-0.11
B6_jason_reseq	-2.013	0.428
MHCII_jason_reseq	-0.114	0.874
Isoniazid02	0.038	1.013
Rifampicin4	1.313	-0.171
Ethambutol3	0.094	0.06
Meropenem3	-0.272	0.159
Vancomycin16	0.459	-0.106
Rv2680_day32	-2.775	-0.055
H37Rv_KO_MarP	0.058	0.876
hypoxia_3wks	-1.105	0.0
hypoxia_6wks	-2.019	-0.299
glycerol	1.978	1.122
cholesterol	0.395	0.722
AJ	-0.474	0.368
Bibs02	1.542	-0.371
Bibs02c	1.002	0.394
BL6	-2.113	-1.865
BL6a	-0.317	-0.342
BXD01	-2.25	-1.648
BXD010	-1.72	-1.35
BXD011	-1.781	-1.534
BXD03	-0.529	-1.12
BXD04	-2.461	-1.647
BXD05	-1.403	-0.946
BXD06	-2.796	-1.222
BXD07	-2.058	-1.3
BXD08	-1.469	-1.139
BXD09	-1.926	-1.068
CAST	-0.976	-0.661
CCcont	-2.22	-1.205
DS01	0.801	0.022
DS02	0.917	-0.391
DS04	0.921	0.475
DS0c	0.185	-0.035
GP01	-0.848	0.67
GP02	0.321	0.046
GP0c	-0.822	0.522
NOD	1.842	0.145
NZO	-0.302	-0.539
PWK	0.099	-0.826
H37Rv_KO_CtpC	-0.317	-1.043
H37Rv_KO_CtpD	-3.057	-1.512
H37Rv_KO_Rv1272	-0.799	-1.109
H37Rv_KO_SugABC	-0.184	0.948
H37Rv_KO_MbtN	0.873	0.311
Trans05	0.443	-1.4
macrophage_unactivated	-2.38	0.249
IL1	-0.759	-0.024
Rapamycin	-1.522	0.43
Tcell	-2.457	-0.971
GMCSF	0.256	0.042
IFNab	0.0	0.239
IFNg	-2.015	-0.224
IFNg_GMCSF1	0.258	0.575
Rv1432_day32	0.795	0.095
Rv1565c_day32	-2.342	0.485
secA2_input	0.822	0.106
delta_Rv3594	1.325	0.965
delta_Rv3717	0.381	1.072
delta_Rv3811	-2.583	1.184
delta_Rv0954	0.34	1.26
PonA1	-0.419	0.965
EccD1_KO	-0.405	0.562
EspI_KO	-2.056	0.502
PE35_KO	-1.52	0.16
PPE68_KO	-1.059	0.474
glycerol2	-1.808	-1.033
lignocerate	-0.994	-0.669
oleate	-2.836	-0.88
phosphatidylcholine	-1.922	-0.819
acetate	-0.289	0.318
glucAc	-0.903	0.0
Rv0950ko	-0.709	-0.151
Rv1096ko	-1.291	0.106
Rv3684ko	-2.99	-0.747
delta_otsA_trehalose	-0.564	0.132