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 Rv2958c/-

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

	Rv1800/PPE28	Rv2958c/-
Fe_supp_jason_reseq	-0.786	0.218
low_pH_jason_reseq	-0.224	-0.591
NO_jason_reseq	-0.123	-0.412
B6_jason_reseq	-0.969	-0.317
MHCII_jason_reseq	-0.668	0.082
Isoniazid02	0.907	0.674
Rifampicin4	0.162	0.103
Ethambutol3	1.313	0.818
Meropenem3	0.637	0.367
Vancomycin16	0.263	0.257
Rv2680_day32	-1.145	0.459
H37Rv_KO_MarP	-0.168	0.464
hypoxia_3wks	-0.199	0.016
hypoxia_6wks	0.157	-0.495
glycerol	-0.532	-1.678
cholesterol	-0.159	-0.524
AJ	0.358	0.212
Bibs02	0.282	0.257
Bibs02c	0.244	0.382
BL6	0.146	-0.448
BL6a	-0.126	0.211
BXD01	-0.096	-0.022
BXD010	0.111	0.164
BXD011	0.618	0.071
BXD03	-0.441	-0.041
BXD04	0.069	0.179
BXD05	-0.199	0.198
BXD06	-0.273	-0.162
BXD07	-0.02	-0.105
BXD08	-0.032	0.008
BXD09	-0.192	-0.21
CAST	0.189	0.092
CCcont	-0.043	-0.071
DS01	-0.286	0.269
DS02	-0.095	0.263
DS04	0.291	0.548
DS0c	-0.308	0.225
GP01	0.845	0.408
GP02	0.832	0.959
GP0c	0.124	-0.35
NOD	0.052	0.937
NZO	0.308	0.475
PWK	0.303	0.485
H37Rv_KO_CtpC	0.486	0.377
H37Rv_KO_CtpD	0.415	0.694
H37Rv_KO_Rv1272	0.684	0.96
H37Rv_KO_SugABC	0.616	0.495
H37Rv_KO_MbtN	0.574	0.425
Trans05	0.768	1.058
macrophage_unactivated	0.436	0.136
IL1	0.0	-0.744
Rapamycin	-0.049	-0.276
Tcell	0.153	-0.306
GMCSF	0.227	-0.177
IFNab	0.097	-0.414
IFNg	0.107	-0.179
IFNg_GMCSF1	0.148	0.277
Rv1432_day32	0.095	0.365
Rv1565c_day32	0.068	0.303
secA2_input	-0.895	-0.524
delta_Rv3594	0.716	0.366
delta_Rv3717	-0.042	-0.198
delta_Rv3811	0.223	0.26
delta_Rv0954	0.327	-0.059
PonA1	0.089	-0.108
EccD1_KO	-0.303	0.28
EspI_KO	-0.208	0.342
PE35_KO	0.58	0.586
PPE68_KO	0.435	0.394
glycerol2	0.695	0.509
lignocerate	0.631	0.6
oleate	0.503	0.509
phosphatidylcholine	0.748	0.71
acetate	0.0	0.166
glucAc	0.268	0.194
Rv0950ko	0.087	0.066
Rv1096ko	-0.356	-0.682
Rv3684ko	-0.37	-0.465
delta_otsA_trehalose	0.132	0.014