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 Rv3511/PE_PGRS55:

update plot	correlation	link to info on gene
Rv0834c/PE_PGRS14	(cc=0.7185)	info on Rv0834c/PE_PGRS14
Rv3508/PE_PGRS54	(cc=0.6409)	info on Rv3508/PE_PGRS54
Rv3512/PE_PGRS56	(cc=0.5701)	info on Rv3512/PE_PGRS56
Rv0235c/-	(cc=0.5471)	info on Rv0235c/-
Rv3514/PE_PGRS57	(cc=0.5468)	info on Rv3514/PE_PGRS57
Rv3345c/PE_PGRS50	(cc=0.5418)	info on Rv3345c/PE_PGRS50
Rv1891/-	(cc=0.5372)	info on Rv1891/-
Rv0833/PE_PGRS13	(cc=0.5355)	info on Rv0833/PE_PGRS13
Rv3394c/-	(cc=0.5008)	info on Rv3394c/-
Rv0354c/PPE7	(cc=0.5006)	info on Rv0354c/PPE7

Correlation of Rv3511/PE_PGRS55 with Rv0354c/PPE7

Normalized LFCs for Rv3511/PE_PGRS55:
(description and provenance of datasets)

	Rv3511/PE_PGRS55	Rv0354c/PPE7
Fe_supp_jason_reseq	-0.718	0.131
low_pH_jason_reseq	-0.269	-1.047
NO_jason_reseq	-0.278	-0.26
B6_jason_reseq	-0.682	-1.113
MHCII_jason_reseq	0.111	-1.462
Isoniazid02	-1.059	-1.225
Rifampicin4	0.444	0.181
Ethambutol3	-0.565	-0.63
Meropenem3	-0.213	-0.53
Vancomycin16	-0.348	-0.406
Rv2680_day32	-0.922	0.453
H37Rv_KO_MarP	0.014	-0.322
hypoxia_3wks	-0.618	-0.455
hypoxia_6wks	-1.347	-0.593
glycerol	0.686	0.809
cholesterol	0.429	0.709
AJ	0.844	0.746
Bibs02	-0.334	0.278
Bibs02c	0.685	0.799
BL6	-0.228	1.261
BL6a	0.321	1.124
BXD01	0.31	0.426
BXD010	-0.196	1.7
BXD011	-0.297	0.983
BXD03	1.067	0.504
BXD04	0.287	0.365
BXD05	0.589	0.909
BXD06	0.178	0.539
BXD07	0.41	0.567
BXD08	0.632	0.844
BXD09	0.287	0.76
CAST	0.075	0.506
CCcont	-0.025	0.885
DS01	-0.866	0.376
DS02	-0.112	0.255
DS04	-0.083	-0.247
DS0c	-0.484	-0.306
GP01	0.579	1.33
GP02	1.313	0.727
GP0c	0.699	0.471
NOD	-0.322	0.182
NZO	1.052	1.208
PWK	0.374	-0.242
H37Rv_KO_CtpC	0.561	1.43
H37Rv_KO_CtpD	0.302	1.569
H37Rv_KO_Rv1272	0.058	1.383
H37Rv_KO_SugABC	0.649	-0.546
H37Rv_KO_MbtN	0.319	0.749
Trans05	1.249	1.526
macrophage_unactivated	0.073	0.704
IL1	-0.59	0.217
Rapamycin	-0.611	0.117
Tcell	-0.479	0.388
GMCSF	0.544	-0.222
IFNab	-0.683	-0.369
IFNg	-0.497	0.238
IFNg_GMCSF1	-0.421	0.261
Rv1432_day32	1.036	0.278
Rv1565c_day32	-0.524	-1.978
secA2_input	0.446	0.31
delta_Rv3594	-0.135	-0.011
delta_Rv3717	-0.53	0.052
delta_Rv3811	-0.349	0.281
delta_Rv0954	-0.808	0.439
PonA1	0.0	-0.403
EccD1_KO	0.444	-0.71
EspI_KO	-0.225	-0.362
PE35_KO	-0.63	-0.292
PPE68_KO	-0.733	-0.474
glycerol2	0.248	0.701
lignocerate	0.342	1.011
oleate	0.166	0.384
phosphatidylcholine	0.221	0.727
acetate	-0.057	-0.057
glucAc	-0.023	0.545
Rv0950ko	0.609	1.07
Rv1096ko	0.531	0.353
Rv3684ko	-0.193	0.439
delta_otsA_trehalose	-1.443	-0.642