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 Rv3161c/-

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

	Rv2352c/PPE38	Rv3161c/-
Fe_supp_jason_reseq	0.35	0.153
low_pH_jason_reseq	-1.029	0.293
NO_jason_reseq	-0.491	0.11
B6_jason_reseq	-0.488	-0.414
MHCII_jason_reseq	-0.46	-0.538
Isoniazid02	-1.043	-0.509
Rifampicin4	-0.208	-0.03
Ethambutol3	-0.882	-0.409
Meropenem3	-1.085	-0.068
Vancomycin16	-0.602	0.088
Rv2680_day32	-0.611	-0.422
H37Rv_KO_MarP	-0.629	0.454
hypoxia_3wks	-0.06	-0.052
hypoxia_6wks	-0.56	-0.338
glycerol	0.532	1.001
cholesterol	0.575	0.628
AJ	0.321	0.244
Bibs02	0.203	0.695
Bibs02c	0.297	0.653
BL6	0.173	0.376
BL6a	0.425	0.798
BXD01	0.346	0.859
BXD010	-0.031	1.108
BXD011	-0.232	0.84
BXD03	0.503	1.053
BXD04	0.661	0.896
BXD05	0.358	0.864
BXD06	0.167	0.369
BXD07	0.22	0.332
BXD08	0.298	0.748
BXD09	0.376	0.319
CAST	0.235	0.242
CCcont	-0.032	0.648
DS01	0.267	0.625
DS02	0.17	-0.142
DS04	0.554	0.696
DS0c	0.179	0.198
GP01	0.253	0.761
GP02	0.349	0.985
GP0c	0.348	1.527
NOD	-0.184	0.138
NZO	0.393	0.527
PWK	0.06	0.612
H37Rv_KO_CtpC	0.169	1.504
H37Rv_KO_CtpD	0.659	1.284
H37Rv_KO_Rv1272	1.248	1.574
H37Rv_KO_SugABC	0.005	1.01
H37Rv_KO_MbtN	0.457	1.145
Trans05	1.088	1.872
macrophage_unactivated	0.511	0.799
IL1	-0.11	-0.564
Rapamycin	0.037	0.178
Tcell	-0.495	0.127
GMCSF	0.533	2.587
IFNab	0.054	0.345
IFNg	0.088	-0.163
IFNg_GMCSF1	0.364	0.635
Rv1432_day32	0.407	-0.66
Rv1565c_day32	-0.141	0.85
secA2_input	-0.626	0.219
delta_Rv3594	0.583	0.838
delta_Rv3717	-0.374	0.853
delta_Rv3811	0.268	0.779
delta_Rv0954	0.289	0.452
PonA1	0.085	0.77
EccD1_KO	-0.566	0.227
EspI_KO	-0.031	0.998
PE35_KO	0.105	0.543
PPE68_KO	0.275	0.902
glycerol2	0.167	0.275
lignocerate	-0.169	0.332
oleate	-0.004	0.713
phosphatidylcholine	-0.224	0.664
acetate	-0.047	-0.246
glucAc	0.016	-0.514
Rv0950ko	0.277	-0.582
Rv1096ko	-0.012	-0.413
Rv3684ko	-0.134	-0.033
delta_otsA_trehalose	0.184	0.371