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 Rv3238c/-

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

	Rv1800/PPE28	Rv3238c/-
Fe_supp_jason_reseq	-0.786	-0.284
low_pH_jason_reseq	-0.224	-1.181
NO_jason_reseq	-0.123	-0.412
B6_jason_reseq	-0.969	-0.232
MHCII_jason_reseq	-0.668	0.04
Isoniazid02	0.907	0.583
Rifampicin4	0.162	0.412
Ethambutol3	1.313	1.198
Meropenem3	0.637	0.873
Vancomycin16	0.263	0.09
Rv2680_day32	-1.145	-0.093
H37Rv_KO_MarP	-0.168	0.426
hypoxia_3wks	-0.199	-0.227
hypoxia_6wks	0.157	0.019
glycerol	-0.532	-0.834
cholesterol	-0.159	-0.074
AJ	0.358	0.282
Bibs02	0.282	-0.57
Bibs02c	0.244	0.441
BL6	0.146	-0.079
BL6a	-0.126	0.184
BXD01	-0.096	0.159
BXD010	0.111	-0.315
BXD011	0.618	0.0
BXD03	-0.441	0.249
BXD04	0.069	0.702
BXD05	-0.199	-0.225
BXD06	-0.273	0.249
BXD07	-0.02	0.174
BXD08	-0.032	-0.2
BXD09	-0.192	-0.041
CAST	0.189	0.082
CCcont	-0.043	0.031
DS01	-0.286	0.14
DS02	-0.095	0.307
DS04	0.291	0.72
DS0c	-0.308	0.399
GP01	0.845	0.234
GP02	0.832	0.51
GP0c	0.124	-0.267
NOD	0.052	0.519
NZO	0.308	-0.202
PWK	0.303	0.59
H37Rv_KO_CtpC	0.486	0.781
H37Rv_KO_CtpD	0.415	-0.056
H37Rv_KO_Rv1272	0.684	0.424
H37Rv_KO_SugABC	0.616	0.385
H37Rv_KO_MbtN	0.574	0.479
Trans05	0.768	0.706
macrophage_unactivated	0.436	0.259
IL1	0.0	0.033
Rapamycin	-0.049	0.0
Tcell	0.153	0.055
GMCSF	0.227	0.576
IFNab	0.097	0.148
IFNg	0.107	0.807
IFNg_GMCSF1	0.148	0.437
Rv1432_day32	0.095	-0.137
Rv1565c_day32	0.068	-0.141
secA2_input	-0.895	-0.507
delta_Rv3594	0.716	0.401
delta_Rv3717	-0.042	-0.059
delta_Rv3811	0.223	-0.15
delta_Rv0954	0.327	0.243
PonA1	0.089	-0.34
EccD1_KO	-0.303	0.316
EspI_KO	-0.208	1.212
PE35_KO	0.58	1.03
PPE68_KO	0.435	1.088
glycerol2	0.695	0.502
lignocerate	0.631	0.514
oleate	0.503	0.625
phosphatidylcholine	0.748	0.501
acetate	0.0	0.105
glucAc	0.268	0.016
Rv0950ko	0.087	0.289
Rv1096ko	-0.356	-0.166
Rv3684ko	-0.37	0.727
delta_otsA_trehalose	0.132	-0.38