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 Rv3394c/-

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

	Rv3511/PE_PGRS55	Rv3394c/-
Fe_supp_jason_reseq	-0.718	-0.829
low_pH_jason_reseq	-0.269	1.228
NO_jason_reseq	-0.278	0.591
B6_jason_reseq	-0.682	-1.269
MHCII_jason_reseq	0.111	-0.58
Isoniazid02	-1.059	-0.339
Rifampicin4	0.444	0.72
Ethambutol3	-0.565	-0.197
Meropenem3	-0.213	0.207
Vancomycin16	-0.348	0.0
Rv2680_day32	-0.922	-0.422
H37Rv_KO_MarP	0.014	0.289
hypoxia_3wks	-0.618	0.439
hypoxia_6wks	-1.347	-0.048
glycerol	0.686	2.058
cholesterol	0.429	1.696
AJ	0.844	1.627
Bibs02	-0.334	0.0
Bibs02c	0.685	0.756
BL6	-0.228	0.16
BL6a	0.321	0.443
BXD01	0.31	0.029
BXD010	-0.196	0.4
BXD011	-0.297	0.137
BXD03	1.067	0.399
BXD04	0.287	0.486
BXD05	0.589	0.373
BXD06	0.178	0.417
BXD07	0.41	0.232
BXD08	0.632	1.2
BXD09	0.287	0.39
CAST	0.075	0.385
CCcont	-0.025	0.677
DS01	-0.866	0.777
DS02	-0.112	0.364
DS04	-0.083	1.147
DS0c	-0.484	-0.823
GP01	0.579	1.305
GP02	1.313	1.89
GP0c	0.699	0.769
NOD	-0.322	-0.158
NZO	1.052	0.446
PWK	0.374	0.0
H37Rv_KO_CtpC	0.561	0.587
H37Rv_KO_CtpD	0.302	0.351
H37Rv_KO_Rv1272	0.058	1.115
H37Rv_KO_SugABC	0.649	0.659
H37Rv_KO_MbtN	0.319	-0.024
Trans05	1.249	1.567
macrophage_unactivated	0.073	-0.114
IL1	-0.59	0.727
Rapamycin	-0.611	-0.055
Tcell	-0.479	-0.554
GMCSF	0.544	0.317
IFNab	-0.683	-0.109
IFNg	-0.497	0.406
IFNg_GMCSF1	-0.421	1.09
Rv1432_day32	1.036	1.112
Rv1565c_day32	-0.524	1.887
secA2_input	0.446	0.269
delta_Rv3594	-0.135	-0.078
delta_Rv3717	-0.53	0.062
delta_Rv3811	-0.349	0.073
delta_Rv0954	-0.808	0.124
PonA1	0.0	0.329
EccD1_KO	0.444	0.753
EspI_KO	-0.225	-0.322
PE35_KO	-0.63	-0.137
PPE68_KO	-0.733	0.099
glycerol2	0.248	-0.059
lignocerate	0.342	0.499
oleate	0.166	0.274
phosphatidylcholine	0.221	0.296
acetate	-0.057	0.733
glucAc	-0.023	0.307
Rv0950ko	0.609	0.1
Rv1096ko	0.531	0.473
Rv3684ko	-0.193	1.52
delta_otsA_trehalose	-1.443	-0.045