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 Rv2782c/pepR:

update plot	correlation	link to info on gene
Rv2684/arsA	(cc=0.5982)	info on Rv2684/arsA
Rv2335/cysE	(cc=0.5932)	info on Rv2335/cysE
Rv2901c/-	(cc=0.534)	info on Rv2901c/-
Rv2683/-	(cc=0.5318)	info on Rv2683/-
Rv0554/bpoC	(cc=0.4911)	info on Rv0554/bpoC
Rv1286/cysN	(cc=0.4794)	info on Rv1286/cysN
Rv2334/cysK1	(cc=0.4745)	info on Rv2334/cysK1
Rv1100/-	(cc=0.4662)	info on Rv1100/-
Rv2795c/-	(cc=0.4492)	info on Rv2795c/-
Rv2581c/-	(cc=0.4484)	info on Rv2581c/-

Correlation of Rv2782c/pepR with Rv2334/cysK1

Normalized LFCs for Rv2782c/pepR:
(description and provenance of datasets)

	Rv2782c/pepR	Rv2334/cysK1
Fe_supp_jason_reseq	1.5	2.437
low_pH_jason_reseq	0.39	5.069
NO_jason_reseq	-0.549	1.089
B6_jason_reseq	0.514	0.357
MHCII_jason_reseq	0.337	-0.257
Isoniazid02	0.348	3.403
Rifampicin4	1.584	0.634
Ethambutol3	-0.035	0.285
Meropenem3	2.27	-0.335
Vancomycin16	0.883	0.809
Rv2680_day32	0.997	0.0
H37Rv_KO_MarP	-1.089	1.666
hypoxia_3wks	-2.408	-1.284
hypoxia_6wks	-1.693	0.378
glycerol	-0.546	2.455
cholesterol	-0.972	1.761
AJ	-0.442	0.232
Bibs02	-0.629	0.0
Bibs02c	0.671	0.0
BL6	0.865	0.53
BL6a	0.304	1.435
BXD01	0.364	2.245
BXD010	0.454	1.115
BXD011	-0.161	0.626
BXD03	0.722	1.351
BXD04	-0.07	1.184
BXD05	0.503	1.109
BXD06	0.316	1.485
BXD07	0.49	0.768
BXD08	0.128	2.419
BXD09	0.248	0.863
CAST	0.062	3.337
CCcont	0.428	1.492
DS01	0.147	0.45
DS02	0.854	0.217
DS04	-0.594	0.37
DS0c	-1.455	0.0
GP01	-1.525	0.0
GP02	-0.544	0.0
GP0c	-1.493	0.0
NOD	-0.332	1.507
NZO	0.053	0.0
PWK	0.205	0.196
H37Rv_KO_CtpC	-0.172	0.0
H37Rv_KO_CtpD	0.648	0.703
H37Rv_KO_Rv1272	-0.805	0.269
H37Rv_KO_SugABC	-0.505	0.664
H37Rv_KO_MbtN	-1.475	0.283
Trans05	-0.81	0.803
macrophage_unactivated	-0.966	0.398
IL1	0.128	-0.409
Rapamycin	-0.39	-0.424
Tcell	0.072	-0.45
GMCSF	-1.146	0.0
IFNab	-2.373	-0.417
IFNg	-1.622	-0.369
IFNg_GMCSF1	-1.804	0.0
Rv1432_day32	-0.15	-0.18
Rv1565c_day32	-0.425	1.507
secA2_input	-1.34	-1.315
delta_Rv3594	-1.869	-2.522
delta_Rv3717	-3.01	-2.896
delta_Rv3811	-2.162	-2.767
delta_Rv0954	-0.376	-0.716
PonA1	0.279	0.864
EccD1_KO	0.056	0.526
EspI_KO	-0.87	2.053
PE35_KO	1.135	0.683
PPE68_KO	0.368	1.59
glycerol2	-0.566	-1.208
lignocerate	-1.579	-0.756
oleate	-3.088	-1.418
phosphatidylcholine	-0.695	-1.401
acetate	0.081	0.72
glucAc	0.18	0.272
Rv0950ko	-0.757	1.999
Rv1096ko	-0.437	2.925
Rv3684ko	0.478	2.044
delta_otsA_trehalose	0.179	0.854