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 Rv1920/-

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

	Rv1800/PPE28	Rv1920/-
Fe_supp_jason_reseq	-0.786	-1.601
low_pH_jason_reseq	-0.224	-0.201
NO_jason_reseq	-0.123	-0.383
B6_jason_reseq	-0.969	-0.487
MHCII_jason_reseq	-0.668	-1.332
Isoniazid02	0.907	-0.061
Rifampicin4	0.162	0.217
Ethambutol3	1.313	-0.094
Meropenem3	0.637	0.294
Vancomycin16	0.263	-0.093
Rv2680_day32	-1.145	-0.545
H37Rv_KO_MarP	-0.168	-0.207
hypoxia_3wks	-0.199	0.658
hypoxia_6wks	0.157	0.791
glycerol	-0.532	-0.581
cholesterol	-0.159	-0.301
AJ	0.358	0.687
Bibs02	0.282	0.062
Bibs02c	0.244	-0.174
BL6	0.146	-0.135
BL6a	-0.126	0.276
BXD01	-0.096	-0.271
BXD010	0.111	0.139
BXD011	0.618	0.064
BXD03	-0.441	-0.096
BXD04	0.069	-0.014
BXD05	-0.199	0.06
BXD06	-0.273	0.102
BXD07	-0.02	0.331
BXD08	-0.032	0.123
BXD09	-0.192	0.216
CAST	0.189	0.202
CCcont	-0.043	-0.487
DS01	-0.286	0.169
DS02	-0.095	-0.194
DS04	0.291	-0.298
DS0c	-0.308	-0.063
GP01	0.845	1.29
GP02	0.832	-0.999
GP0c	0.124	-0.62
NOD	0.052	-0.628
NZO	0.308	0.988
PWK	0.303	-0.594
H37Rv_KO_CtpC	0.486	0.241
H37Rv_KO_CtpD	0.415	0.851
H37Rv_KO_Rv1272	0.684	1.096
H37Rv_KO_SugABC	0.616	-0.058
H37Rv_KO_MbtN	0.574	0.832
Trans05	0.768	0.825
macrophage_unactivated	0.436	1.146
IL1	0.0	-0.021
Rapamycin	-0.049	0.043
Tcell	0.153	-0.3
GMCSF	0.227	1.001
IFNab	0.097	0.396
IFNg	0.107	0.925
IFNg_GMCSF1	0.148	0.393
Rv1432_day32	0.095	0.267
Rv1565c_day32	0.068	0.438
secA2_input	-0.895	-1.273
delta_Rv3594	0.716	-0.035
delta_Rv3717	-0.042	0.216
delta_Rv3811	0.223	0.0
delta_Rv0954	0.327	-0.801
PonA1	0.089	-0.298
EccD1_KO	-0.303	-0.418
EspI_KO	-0.208	-0.168
PE35_KO	0.58	-0.128
PPE68_KO	0.435	0.643
glycerol2	0.695	0.377
lignocerate	0.631	0.188
oleate	0.503	0.302
phosphatidylcholine	0.748	0.751
acetate	0.0	-0.048
glucAc	0.268	-0.178
Rv0950ko	0.087	-1.279
Rv1096ko	-0.356	-1.224
Rv3684ko	-0.37	-1.035
delta_otsA_trehalose	0.132	1.142