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 Rv3512/PE_PGRS56:

update plot	correlation	link to info on gene
Rv1087/PE_PGRS21	(cc=0.7395)	info on Rv1087/PE_PGRS21
Rv3508/PE_PGRS54	(cc=0.7258)	info on Rv3508/PE_PGRS54
Rv3514/PE_PGRS57	(cc=0.7087)	info on Rv3514/PE_PGRS57
Rv1091/PE_PGRS22	(cc=0.6852)	info on Rv1091/PE_PGRS22
Rv3345c/PE_PGRS50	(cc=0.6749)	info on Rv3345c/PE_PGRS50
Rv0833/PE_PGRS13	(cc=0.6545)	info on Rv0833/PE_PGRS13
Rv2815c/-	(cc=0.5911)	info on Rv2815c/-
Rv3511/PE_PGRS55	(cc=0.5701)	info on Rv3511/PE_PGRS55
Rv2479c/-	(cc=0.5599)	info on Rv2479c/-
Rv2814c/-	(cc=0.5554)	info on Rv2814c/-

Correlation of Rv3512/PE_PGRS56 with Rv0833/PE_PGRS13

Normalized LFCs for Rv3512/PE_PGRS56:
(description and provenance of datasets)

	Rv3512/PE_PGRS56	Rv0833/PE_PGRS13
Fe_supp_jason_reseq	-0.587	-0.923
low_pH_jason_reseq	-1.091	-0.284
NO_jason_reseq	-0.176	0.205
B6_jason_reseq	-0.322	-0.52
MHCII_jason_reseq	0.123	-0.694
Isoniazid02	-1.909	0.469
Rifampicin4	-0.647	0.872
Ethambutol3	-0.537	0.27
Meropenem3	-0.737	0.0
Vancomycin16	-0.963	0.589
Rv2680_day32	0.529	-0.082
H37Rv_KO_MarP	0.0	-0.525
hypoxia_3wks	-0.183	0.706
hypoxia_6wks	-1.13	-0.274
glycerol	1.981	0.686
cholesterol	1.209	0.574
AJ	2.276	1.771
Bibs02	1.27	0.621
Bibs02c	1.576	1.678
BL6	0.263	-0.104
BL6a	0.914	0.993
BXD01	0.695	0.101
BXD010	1.102	0.928
BXD011	0.49	0.0
BXD03	0.573	1.084
BXD04	0.859	0.793
BXD05	0.764	0.377
BXD06	0.075	0.199
BXD07	0.291	0.301
BXD08	0.341	0.452
BXD09	0.36	0.305
CAST	0.484	0.782
CCcont	0.24	-0.124
DS01	0.38	-0.412
DS02	0.922	0.0
DS04	0.11	0.0
DS0c	-0.129	-0.379
GP01	0.561	1.185
GP02	0.553	2.978
GP0c	0.738	1.594
NOD	0.0	1.884
NZO	1.326	0.298
PWK	0.674	0.426
H37Rv_KO_CtpC	0.261	0.353
H37Rv_KO_CtpD	0.584	0.635
H37Rv_KO_Rv1272	1.177	0.479
H37Rv_KO_SugABC	0.381	-0.272
H37Rv_KO_MbtN	-0.271	-0.283
Trans05	1.157	0.588
macrophage_unactivated	-0.537	-0.783
IL1	-1.978	-1.967
Rapamycin	-1.795	-1.679
Tcell	-1.652	-1.782
GMCSF	-0.779	-0.422
IFNab	-2.283	-2.382
IFNg	-1.157	-0.911
IFNg_GMCSF1	-0.349	-1.071
Rv1432_day32	0.252	0.661
Rv1565c_day32	-1.275	-1.054
secA2_input	0.0	-0.861
delta_Rv3594	0.272	0.0
delta_Rv3717	-0.629	-0.508
delta_Rv3811	-0.253	-0.149
delta_Rv0954	-2.288	-1.333
PonA1	0.714	0.451
EccD1_KO	0.418	0.49
EspI_KO	-0.451	0.26
PE35_KO	-0.916	-0.283
PPE68_KO	-0.685	-0.205
glycerol2	0.109	-0.392
lignocerate	0.505	-0.613
oleate	-0.515	-0.397
phosphatidylcholine	0.0	-0.253
acetate	1.225	0.507
glucAc	1.367	0.165
Rv0950ko	-0.63	0.621
Rv1096ko	0.115	1.08
Rv3684ko	-0.065	0.462
delta_otsA_trehalose	0.366	0.0