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 Rv1088/PE9:

update plot	correlation	link to info on gene
Rv1918c/PPE35	(cc=0.6152)	info on Rv1918c/PPE35
Rv2548/vapC19	(cc=0.5699)	info on Rv2548/vapC19
Rv2717c/-	(cc=0.5658)	info on Rv2717c/-
Rv1059/-	(cc=0.5656)	info on Rv1059/-
Rv0799c/-	(cc=0.5429)	info on Rv0799c/-
Rv1521/fadD25	(cc=0.5388)	info on Rv1521/fadD25
Rv0260c/-	(cc=0.5319)	info on Rv0260c/-
Rv1502/-	(cc=0.5291)	info on Rv1502/-
Rv2835c/ugpA	(cc=0.5128)	info on Rv2835c/ugpA
Rv2809/-	(cc=0.5059)	info on Rv2809/-

Correlation of Rv1088/PE9 with Rv2717c/-

Normalized LFCs for Rv1088/PE9:
(description and provenance of datasets)

	Rv1088/PE9	Rv2717c/-
Fe_supp_jason_reseq	1.621	0.474
low_pH_jason_reseq	-2.414	-0.611
NO_jason_reseq	-0.108	-0.081
B6_jason_reseq	-0.142	-0.14
MHCII_jason_reseq	-1.374	-1.399
Isoniazid02	0.534	0.1
Rifampicin4	1.037	-0.097
Ethambutol3	0.505	0.103
Meropenem3	1.364	1.193
Vancomycin16	0.268	0.0
Rv2680_day32	-3.328	-1.824
H37Rv_KO_MarP	-0.277	-0.409
hypoxia_3wks	0.299	0.08
hypoxia_6wks	0.021	-0.33
glycerol	-2.147	-0.774
cholesterol	-0.961	-0.055
AJ	-0.827	1.276
Bibs02	0.842	0.093
Bibs02c	-0.981	-0.265
BL6	0.674	1.014
BL6a	1.459	0.917
BXD01	1.37	1.27
BXD010	1.021	-0.217
BXD011	1.285	0.448
BXD03	1.652	0.291
BXD04	0.061	0.905
BXD05	1.745	0.509
BXD06	1.016	1.179
BXD07	0.866	1.029
BXD08	1.823	0.702
BXD09	1.547	0.32
CAST	-0.445	1.131
CCcont	0.882	0.879
DS01	-1.567	0.702
DS02	0.21	0.441
DS04	-0.316	0.576
DS0c	-1.439	-0.63
GP01	-1.37	-0.177
GP02	-0.065	1.036
GP0c	0.253	0.215
NOD	-1.189	1.019
NZO	0.87	-0.107
PWK	-1.445	0.209
H37Rv_KO_CtpC	0.971	-0.139
H37Rv_KO_CtpD	0.683	0.28
H37Rv_KO_Rv1272	1.354	0.775
H37Rv_KO_SugABC	0.606	0.571
H37Rv_KO_MbtN	-0.659	-0.362
Trans05	2.476	0.803
macrophage_unactivated	0.707	1.382
IL1	0.406	0.285
Rapamycin	0.663	-0.209
Tcell	1.896	0.235
GMCSF	0.446	0.747
IFNab	0.106	0.517
IFNg	0.759	-0.321
IFNg_GMCSF1	-0.569	0.716
Rv1432_day32	0.265	0.253
Rv1565c_day32	0.414	0.344
secA2_input	-1.772	-0.571
delta_Rv3594	-0.278	0.564
delta_Rv3717	0.54	-0.028
delta_Rv3811	0.776	0.094
delta_Rv0954	-0.631	-0.269
PonA1	-0.248	0.555
EccD1_KO	-0.707	-0.299
EspI_KO	0.0	-0.505
PE35_KO	-1.683	0.685
PPE68_KO	-1.11	0.477
glycerol2	0.266	0.713
lignocerate	0.911	0.684
oleate	-0.588	0.301
phosphatidylcholine	0.585	0.927
acetate	0.198	0.46
glucAc	0.484	0.4
Rv0950ko	-0.992	-0.95
Rv1096ko	-3.016	-1.134
Rv3684ko	-2.738	-1.411
delta_otsA_trehalose	0.539	0.26