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 Rv0109/PE_PGRS1:

update plot	correlation	link to info on gene
Rv1471/trxB1	(cc=0.5578)	info on Rv1471/trxB1
Rv0349/-	(cc=0.5432)	info on Rv0349/-
Rv3143/-	(cc=0.5339)	info on Rv3143/-
Rv3232c/ppk2	(cc=0.521)	info on Rv3232c/ppk2
Rv2317/uspB	(cc=0.5163)	info on Rv2317/uspB
Rv0042c/-	(cc=0.5114)	info on Rv0042c/-
Rv2147c/-	(cc=0.5005)	info on Rv2147c/-
Rv2842c/-	(cc=0.4974)	info on Rv2842c/-
Rv3149/nuoE	(cc=0.483)	info on Rv3149/nuoE
Rv3152/nuoH	(cc=0.4813)	info on Rv3152/nuoH

Correlation of Rv0109/PE_PGRS1 with Rv3143/-

Normalized LFCs for Rv0109/PE_PGRS1:
(description and provenance of datasets)

	Rv0109/PE_PGRS1	Rv3143/-
Fe_supp_jason_reseq	-1.609	-1.877
low_pH_jason_reseq	0.646	-1.143
NO_jason_reseq	-0.541	-1.208
B6_jason_reseq	-1.364	-4.188
MHCII_jason_reseq	-0.516	-1.39
Isoniazid02	-0.626	0.266
Rifampicin4	-0.181	-0.295
Ethambutol3	-0.054	-0.298
Meropenem3	0.026	0.313
Vancomycin16	-0.239	0.117
Rv2680_day32	0.271	-0.985
H37Rv_KO_MarP	-0.349	-0.346
hypoxia_3wks	-0.367	0.471
hypoxia_6wks	-0.731	-0.793
glycerol	-1.001	-2.776
cholesterol	-0.034	-0.689
AJ	0.156	0.116
Bibs02	-0.535	0.177
Bibs02c	-0.1	-0.285
BL6	1.203	1.687
BL6a	0.663	1.581
BXD01	1.074	1.228
BXD010	0.882	3.555
BXD011	1.237	2.162
BXD03	0.407	1.924
BXD04	0.711	1.727
BXD05	1.095	3.618
BXD06	0.675	1.509
BXD07	1.294	2.527
BXD08	0.533	1.527
BXD09	0.789	2.053
CAST	0.205	-0.918
CCcont	1.465	1.801
DS01	-0.229	0.725
DS02	0.372	2.759
DS04	0.131	2.292
DS0c	-0.211	1.045
GP01	-0.787	1.656
GP02	-0.705	2.771
GP0c	0.345	2.04
NOD	-0.107	-2.696
NZO	0.668	-0.272
PWK	-0.142	-2.062
H37Rv_KO_CtpC	-0.038	0.588
H37Rv_KO_CtpD	0.778	1.365
H37Rv_KO_Rv1272	1.344	0.909
H37Rv_KO_SugABC	0.857	3.633
H37Rv_KO_MbtN	-0.211	-0.373
Trans05	1.68	2.717
macrophage_unactivated	0.429	0.65
IL1	0.184	-0.712
Rapamycin	-0.098	-0.951
Tcell	-0.489	0.111
GMCSF	-0.084	0.296
IFNab	0.048	0.339
IFNg	0.246	0.091
IFNg_GMCSF1	0.776	-0.503
Rv1432_day32	1.119	1.781
Rv1565c_day32	0.115	0.0
secA2_input	-0.045	-1.623
delta_Rv3594	1.127	0.653
delta_Rv3717	1.333	0.229
delta_Rv3811	0.909	-1.331
delta_Rv0954	0.721	1.12
PonA1	0.705	-0.34
EccD1_KO	1.089	0.806
EspI_KO	-0.53	-0.428
PE35_KO	-0.403	0.738
PPE68_KO	-0.288	0.461
glycerol2	0.82	1.648
lignocerate	0.872	-0.207
oleate	0.048	0.645
phosphatidylcholine	0.471	-0.324
acetate	0.934	1.662
glucAc	1.169	0.253
Rv0950ko	1.022	-0.962
Rv1096ko	0.582	0.932
Rv3684ko	0.796	0.21
delta_otsA_trehalose	0.536	1.437