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 Rv2352c/PPE38:

update plot	correlation	link to info on gene
Rv0160c/PE4	(cc=0.5845)	info on Rv0160c/PE4
Rv3161c/-	(cc=0.5722)	info on Rv3161c/-
Rv0354c/PPE7	(cc=0.5707)	info on Rv0354c/PPE7
Rv1504c/-	(cc=0.5614)	info on Rv1504c/-
Rv2947c/pks15	(cc=0.5506)	info on Rv2947c/pks15
Rv1278/-	(cc=0.5437)	info on Rv1278/-
Rv3919c/gid	(cc=0.5421)	info on Rv3919c/gid
Rv0073/-	(cc=0.5416)	info on Rv0073/-
Rv0469/umaA	(cc=0.5381)	info on Rv0469/umaA
Rv2853/PE_PGRS48	(cc=0.5372)	info on Rv2853/PE_PGRS48

Correlation of Rv2352c/PPE38 with Rv1504c/-

Normalized LFCs for Rv2352c/PPE38:
(description and provenance of datasets)

	Rv2352c/PPE38	Rv1504c/-
Fe_supp_jason_reseq	0.35	0.161
low_pH_jason_reseq	-1.029	-0.294
NO_jason_reseq	-0.491	-0.11
B6_jason_reseq	-0.488	-0.505
MHCII_jason_reseq	-0.46	0.005
Isoniazid02	-1.043	0.047
Rifampicin4	-0.208	-0.349
Ethambutol3	-0.882	-0.06
Meropenem3	-1.085	-0.034
Vancomycin16	-0.602	-0.218
Rv2680_day32	-0.611	-0.607
H37Rv_KO_MarP	-0.629	-0.364
hypoxia_3wks	-0.06	0.471
hypoxia_6wks	-0.56	0.255
glycerol	0.532	0.284
cholesterol	0.575	0.316
AJ	0.321	0.429
Bibs02	0.203	0.677
Bibs02c	0.297	0.218
BL6	0.173	1.455
BL6a	0.425	1.218
BXD01	0.346	0.632
BXD010	-0.031	1.204
BXD011	-0.232	1.111
BXD03	0.503	1.778
BXD04	0.661	1.499
BXD05	0.358	1.413
BXD06	0.167	0.825
BXD07	0.22	1.414
BXD08	0.298	1.164
BXD09	0.376	1.357
CAST	0.235	0.649
CCcont	-0.032	0.778
DS01	0.267	1.304
DS02	0.17	1.23
DS04	0.554	1.085
DS0c	0.179	1.669
GP01	0.253	0.956
GP02	0.349	1.205
GP0c	0.348	0.583
NOD	-0.184	-0.586
NZO	0.393	0.787
PWK	0.06	0.409
H37Rv_KO_CtpC	0.169	1.422
H37Rv_KO_CtpD	0.659	1.016
H37Rv_KO_Rv1272	1.248	2.168
H37Rv_KO_SugABC	0.005	0.981
H37Rv_KO_MbtN	0.457	1.97
Trans05	1.088	1.837
macrophage_unactivated	0.511	-0.524
IL1	-0.11	0.053
Rapamycin	0.037	0.068
Tcell	-0.495	0.43
GMCSF	0.533	0.198
IFNab	0.054	-0.215
IFNg	0.088	0.441
IFNg_GMCSF1	0.364	0.352
Rv1432_day32	0.407	0.068
Rv1565c_day32	-0.141	0.687
secA2_input	-0.626	-0.479
delta_Rv3594	0.583	0.575
delta_Rv3717	-0.374	0.503
delta_Rv3811	0.268	0.712
delta_Rv0954	0.289	0.37
PonA1	0.085	0.508
EccD1_KO	-0.566	-0.141
EspI_KO	-0.031	0.488
PE35_KO	0.105	0.543
PPE68_KO	0.275	0.275
glycerol2	0.167	0.433
lignocerate	-0.169	-0.051
oleate	-0.004	0.737
phosphatidylcholine	-0.224	0.678
acetate	-0.047	-0.389
glucAc	0.016	-0.673
Rv0950ko	0.277	-0.567
Rv1096ko	-0.012	-1.378
Rv3684ko	-0.134	-0.796
delta_otsA_trehalose	0.184	0.464