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 Rv3652/PE_PGRS60:

update plot	correlation	link to info on gene
Rv0569/-	(cc=0.5626)	info on Rv0569/-
Rv1736c/narX	(cc=0.5455)	info on Rv1736c/narX
Rv0959/-	(cc=0.5353)	info on Rv0959/-
Rv1940/ribA1	(cc=0.5251)	info on Rv1940/ribA1
Rv2418c/-	(cc=0.5241)	info on Rv2418c/-
Rv2002/fabG3	(cc=0.5229)	info on Rv2002/fabG3
Rv0580c/-	(cc=0.5132)	info on Rv0580c/-
Rv2860c/glnA4	(cc=0.4998)	info on Rv2860c/glnA4
Rv2466c/-	(cc=0.4972)	info on Rv2466c/-
Rv1291c/-	(cc=0.4968)	info on Rv1291c/-

Correlation of Rv3652/PE_PGRS60 with Rv2860c/glnA4

Normalized LFCs for Rv3652/PE_PGRS60:
(description and provenance of datasets)

	Rv3652/PE_PGRS60	Rv2860c/glnA4
Fe_supp_jason_reseq	-0.27	0.272
low_pH_jason_reseq	1.079	0.348
NO_jason_reseq	0.186	-0.163
B6_jason_reseq	0.641	1.016
MHCII_jason_reseq	0.67	1.38
Isoniazid02	0.33	0.528
Rifampicin4	-0.217	-0.206
Ethambutol3	0.169	2.104
Meropenem3	0.153	0.435
Vancomycin16	1.101	0.443
Rv2680_day32	2.801	0.795
H37Rv_KO_MarP	0.104	-0.167
hypoxia_3wks	0.618	-0.144
hypoxia_6wks	0.084	-0.205
glycerol	0.62	0.878
cholesterol	0.779	0.406
AJ	-0.111	0.457
Bibs02	0.699	-0.015
Bibs02c	-0.573	-0.033
BL6	-1.002	-0.438
BL6a	-0.512	-0.29
BXD01	-0.249	0.13
BXD010	-0.837	-0.299
BXD011	-0.305	-0.01
BXD03	-1.399	0.183
BXD04	-0.409	-0.216
BXD05	-0.534	0.309
BXD06	-0.522	-0.124
BXD07	-0.716	-0.057
BXD08	-0.091	0.152
BXD09	-0.683	-0.299
CAST	0.155	0.279
CCcont	-1.008	-0.379
DS01	0.712	1.027
DS02	-0.26	0.61
DS04	0.557	0.904
DS0c	-0.508	1.193
GP01	-0.386	-0.906
GP02	0.445	0.944
GP0c	-0.907	-0.984
NOD	-0.462	-0.308
NZO	0.262	0.535
PWK	-0.618	0.689
H37Rv_KO_CtpC	-2.385	-0.804
H37Rv_KO_CtpD	-1.86	-1.941
H37Rv_KO_Rv1272	-0.668	0.109
H37Rv_KO_SugABC	-1.701	-0.325
H37Rv_KO_MbtN	-0.861	-0.907
Trans05	-1.511	0.292
macrophage_unactivated	0.114	0.679
IL1	1.21	0.383
Rapamycin	-0.377	0.147
Tcell	-0.222	-0.459
GMCSF	0.61	0.28
IFNab	1.233	0.036
IFNg	-0.139	-0.235
IFNg_GMCSF1	0.138	0.151
Rv1432_day32	0.343	0.738
Rv1565c_day32	0.722	-0.3
secA2_input	-0.258	0.715
delta_Rv3594	-0.376	0.142
delta_Rv3717	0.789	0.117
delta_Rv3811	-0.291	-0.274
delta_Rv0954	0.247	-0.578
PonA1	-0.455	0.358
EccD1_KO	0.638	0.441
EspI_KO	0.428	0.168
PE35_KO	1.152	0.598
PPE68_KO	0.729	0.429
glycerol2	0.42	0.158
lignocerate	-0.161	0.138
oleate	0.961	0.73
phosphatidylcholine	0.193	0.556
acetate	-0.091	-0.1
glucAc	-0.6	-0.079
Rv0950ko	-0.226	0.425
Rv1096ko	0.422	0.621
Rv3684ko	0.177	0.622
delta_otsA_trehalose	1.871	0.045