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 Rv0260c/-

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

	Rv1088/PE9	Rv0260c/-
Fe_supp_jason_reseq	1.621	0.305
low_pH_jason_reseq	-2.414	-0.371
NO_jason_reseq	-0.108	0.507
B6_jason_reseq	-0.142	-0.486
MHCII_jason_reseq	-1.374	-0.849
Isoniazid02	0.534	-0.927
Rifampicin4	1.037	-0.942
Ethambutol3	0.505	-0.103
Meropenem3	1.364	-0.325
Vancomycin16	0.268	-0.528
Rv2680_day32	-3.328	-2.041
H37Rv_KO_MarP	-0.277	-0.066
hypoxia_3wks	0.299	-0.187
hypoxia_6wks	0.021	-0.758
glycerol	-2.147	1.044
cholesterol	-0.961	0.421
AJ	-0.827	1.2
Bibs02	0.842	1.673
Bibs02c	-0.981	0.247
BL6	0.674	1.504
BL6a	1.459	1.517
BXD01	1.37	2.017
BXD010	1.021	1.215
BXD011	1.285	0.812
BXD03	1.652	2.181
BXD04	0.061	0.922
BXD05	1.745	0.975
BXD06	1.016	1.198
BXD07	0.866	1.947
BXD08	1.823	1.885
BXD09	1.547	1.31
CAST	-0.445	0.272
CCcont	0.882	2.435
DS01	-1.567	1.451
DS02	0.21	0.764
DS04	-0.316	0.301
DS0c	-1.439	-0.396
GP01	-1.37	1.017
GP02	-0.065	0.409
GP0c	0.253	1.021
NOD	-1.189	0.181
NZO	0.87	0.98
PWK	-1.445	0.57
H37Rv_KO_CtpC	0.971	2.017
H37Rv_KO_CtpD	0.683	1.862
H37Rv_KO_Rv1272	1.354	0.799
H37Rv_KO_SugABC	0.606	1.425
H37Rv_KO_MbtN	-0.659	0.768
Trans05	2.476	1.387
macrophage_unactivated	0.707	0.884
IL1	0.406	0.831
Rapamycin	0.663	0.924
Tcell	1.896	1.114
GMCSF	0.446	0.903
IFNab	0.106	0.783
IFNg	0.759	0.914
IFNg_GMCSF1	-0.569	0.606
Rv1432_day32	0.265	0.705
Rv1565c_day32	0.414	0.834
secA2_input	-1.772	-1.299
delta_Rv3594	-0.278	-1.618
delta_Rv3717	0.54	0.355
delta_Rv3811	0.776	-0.198
delta_Rv0954	-0.631	-1.654
PonA1	-0.248	-2.48
EccD1_KO	-0.707	0.224
EspI_KO	0.0	0.334
PE35_KO	-1.683	-0.54
PPE68_KO	-1.11	0.0
glycerol2	0.266	0.793
lignocerate	0.911	1.195
oleate	-0.588	0.526
phosphatidylcholine	0.585	1.015
acetate	0.198	1.167
glucAc	0.484	1.314
Rv0950ko	-0.992	-0.202
Rv1096ko	-3.016	-0.875
Rv3684ko	-2.738	-0.57
delta_otsA_trehalose	0.539	-0.11