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 Rv1800/PPE28:

update plot	correlation	link to info on gene
Rv2958c/-	(cc=0.5573)	info on Rv2958c/-
Rv2770c/PPE44	(cc=0.5291)	info on Rv2770c/PPE44
Rv1552/frdA	(cc=0.5017)	info on Rv1552/frdA
Rv1951c/-	(cc=0.5009)	info on Rv1951c/-
Rv3238c/-	(cc=0.4983)	info on Rv3238c/-
Rv1920/-	(cc=0.4866)	info on Rv1920/-
Rv2127/ansP1	(cc=0.4759)	info on Rv2127/ansP1
Rv1871c/-	(cc=0.4722)	info on Rv1871c/-
Rv1992c/ctpG	(cc=0.4688)	info on Rv1992c/ctpG
Rv3290c/lat	(cc=0.4666)	info on Rv3290c/lat

Correlation of Rv1800/PPE28 with Rv1552/frdA

Normalized LFCs for Rv1800/PPE28:
(description and provenance of datasets)

	Rv1800/PPE28	Rv1552/frdA
Fe_supp_jason_reseq	-0.786	-0.283
low_pH_jason_reseq	-0.224	0.679
NO_jason_reseq	-0.123	0.097
B6_jason_reseq	-0.969	-0.246
MHCII_jason_reseq	-0.668	-0.375
Isoniazid02	0.907	1.394
Rifampicin4	0.162	0.057
Ethambutol3	1.313	1.083
Meropenem3	0.637	-0.103
Vancomycin16	0.263	0.162
Rv2680_day32	-1.145	0.071
H37Rv_KO_MarP	-0.168	0.275
hypoxia_3wks	-0.199	0.638
hypoxia_6wks	0.157	0.255
glycerol	-0.532	0.0
cholesterol	-0.159	0.219
AJ	0.358	1.106
Bibs02	0.282	0.474
Bibs02c	0.244	0.196
BL6	0.146	0.225
BL6a	-0.126	0.244
BXD01	-0.096	0.252
BXD010	0.111	0.379
BXD011	0.618	0.229
BXD03	-0.441	-0.349
BXD04	0.069	-0.345
BXD05	-0.199	0.106
BXD06	-0.273	-0.067
BXD07	-0.02	0.526
BXD08	-0.032	0.239
BXD09	-0.192	0.252
CAST	0.189	0.0
CCcont	-0.043	0.048
DS01	-0.286	-0.2
DS02	-0.095	-0.852
DS04	0.291	-0.032
DS0c	-0.308	-0.427
GP01	0.845	0.577
GP02	0.832	0.216
GP0c	0.124	0.369
NOD	0.052	1.185
NZO	0.308	0.889
PWK	0.303	0.405
H37Rv_KO_CtpC	0.486	0.824
H37Rv_KO_CtpD	0.415	1.188
H37Rv_KO_Rv1272	0.684	1.044
H37Rv_KO_SugABC	0.616	0.293
H37Rv_KO_MbtN	0.574	0.491
Trans05	0.768	0.701
macrophage_unactivated	0.436	0.268
IL1	0.0	0.605
Rapamycin	-0.049	0.196
Tcell	0.153	0.538
GMCSF	0.227	-0.058
IFNab	0.097	-0.417
IFNg	0.107	-0.305
IFNg_GMCSF1	0.148	0.267
Rv1432_day32	0.095	0.121
Rv1565c_day32	0.068	0.065
secA2_input	-0.895	-0.269
delta_Rv3594	0.716	0.358
delta_Rv3717	-0.042	-0.138
delta_Rv3811	0.223	0.402
delta_Rv0954	0.327	0.326
PonA1	0.089	-0.353
EccD1_KO	-0.303	0.122
EspI_KO	-0.208	0.787
PE35_KO	0.58	0.939
PPE68_KO	0.435	1.078
glycerol2	0.695	0.0
lignocerate	0.631	-0.069
oleate	0.503	0.2
phosphatidylcholine	0.748	0.126
acetate	0.0	0.03
glucAc	0.268	0.128
Rv0950ko	0.087	-0.326
Rv1096ko	-0.356	-0.73
Rv3684ko	-0.37	-1.343
delta_otsA_trehalose	0.132	0.031