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 Rv0073/-

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

	Rv2352c/PPE38	Rv0073/-
Fe_supp_jason_reseq	0.35	-0.133
low_pH_jason_reseq	-1.029	-0.422
NO_jason_reseq	-0.491	-0.761
B6_jason_reseq	-0.488	0.152
MHCII_jason_reseq	-0.46	-0.392
Isoniazid02	-1.043	-1.654
Rifampicin4	-0.208	-0.801
Ethambutol3	-0.882	-0.55
Meropenem3	-1.085	-1.17
Vancomycin16	-0.602	-1.141
Rv2680_day32	-0.611	0.489
H37Rv_KO_MarP	-0.629	0.0
hypoxia_3wks	-0.06	-0.203
hypoxia_6wks	-0.56	-0.244
glycerol	0.532	0.812
cholesterol	0.575	0.242
AJ	0.321	-0.076
Bibs02	0.203	0.755
Bibs02c	0.297	0.915
BL6	0.173	0.766
BL6a	0.425	0.042
BXD01	0.346	0.451
BXD010	-0.031	0.271
BXD011	-0.232	-0.245
BXD03	0.503	0.36
BXD04	0.661	0.559
BXD05	0.358	0.599
BXD06	0.167	0.259
BXD07	0.22	0.015
BXD08	0.298	-0.198
BXD09	0.376	0.235
CAST	0.235	0.143
CCcont	-0.032	-0.04
DS01	0.267	1.3
DS02	0.17	0.553
DS04	0.554	0.41
DS0c	0.179	0.903
GP01	0.253	0.275
GP02	0.349	0.285
GP0c	0.348	-0.336
NOD	-0.184	0.395
NZO	0.393	0.306
PWK	0.06	0.796
H37Rv_KO_CtpC	0.169	0.467
H37Rv_KO_CtpD	0.659	1.33
H37Rv_KO_Rv1272	1.248	0.816
H37Rv_KO_SugABC	0.005	-0.049
H37Rv_KO_MbtN	0.457	-0.225
Trans05	1.088	1.018
macrophage_unactivated	0.511	0.208
IL1	-0.11	0.08
Rapamycin	0.037	0.338
Tcell	-0.495	0.277
GMCSF	0.533	-0.256
IFNab	0.054	-0.187
IFNg	0.088	-0.241
IFNg_GMCSF1	0.364	-0.512
Rv1432_day32	0.407	-0.489
Rv1565c_day32	-0.141	-0.092
secA2_input	-0.626	0.269
delta_Rv3594	0.583	-0.17
delta_Rv3717	-0.374	-0.341
delta_Rv3811	0.268	-0.439
delta_Rv0954	0.289	-0.134
PonA1	0.085	-0.008
EccD1_KO	-0.566	-0.102
EspI_KO	-0.031	0.268
PE35_KO	0.105	0.257
PPE68_KO	0.275	0.531
glycerol2	0.167	0.073
lignocerate	-0.169	-0.323
oleate	-0.004	0.336
phosphatidylcholine	-0.224	0.022
acetate	-0.047	-1.034
glucAc	0.016	-0.98
Rv0950ko	0.277	0.271
Rv1096ko	-0.012	0.305
Rv3684ko	-0.134	-0.698
delta_otsA_trehalose	0.184	-0.232