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 Rv1015c/rplY:

update plot	correlation	link to info on gene
Rv3228/-	(cc=0.6369)	info on Rv3228/-
Rv3248c/sahH	(cc=0.5707)	info on Rv3248c/sahH
Rv1298/rpmE	(cc=0.5424)	info on Rv1298/rpmE
Rv0946c/pgi	(cc=0.5045)	info on Rv0946c/pgi
Rv0526/-	(cc=0.5036)	info on Rv0526/-
Rv3266c/rmlD	(cc=0.4757)	info on Rv3266c/rmlD
Rv1773c/-	(cc=0.4724)	info on Rv1773c/-
Rv0053/rpsF	(cc=0.4665)	info on Rv0053/rpsF
Rv3455c/truA	(cc=0.4663)	info on Rv3455c/truA
Rv1957/-	(cc=0.4592)	info on Rv1957/-

Correlation of Rv1015c/rplY with Rv3228/-

Normalized LFCs for Rv1015c/rplY:
(description and provenance of datasets)

	Rv1015c/rplY	Rv3228/-
Fe_supp_jason_reseq	0.415	0.218
low_pH_jason_reseq	0.0	0.0
NO_jason_reseq	0.0	0.0
B6_jason_reseq	0.0	0.0
MHCII_jason_reseq	0.0	0.0
Isoniazid02	-0.551	0.72
Rifampicin4	1.27	-0.574
Ethambutol3	1.467	1.745
Meropenem3	-0.138	0.648
Vancomycin16	1.451	3.218
Rv2680_day32	0.0	-0.095
H37Rv_KO_MarP	-0.123	2.111
hypoxia_3wks	0.0	0.0
hypoxia_6wks	0.0	0.0
glycerol	0.184	0.709
cholesterol	0.469	0.145
AJ	-0.232	0.232
Bibs02	-0.183	0.0
Bibs02c	-0.209	0.0
BL6	-0.125	0.0
BL6a	-0.198	0.0
BXD01	-0.13	0.0
BXD010	-0.128	0.0
BXD011	-0.127	0.0
BXD03	-0.135	0.0
BXD04	-0.124	0.124
BXD05	0.0	0.0
BXD06	-0.133	0.0
BXD07	-0.138	0.0
BXD08	-0.133	0.133
BXD09	-0.14	0.0
CAST	-0.23	0.0
CCcont	-0.149	1.606
DS01	-0.236	0.0
DS02	-0.217	0.0
DS04	-0.194	0.194
DS0c	-0.217	0.0
GP01	-0.099	0.0
GP02	-0.083	0.0
GP0c	0.0	0.0
NOD	0.205	0.0
NZO	-0.199	0.0
PWK	0.179	0.0
H37Rv_KO_CtpC	-0.162	0.0
H37Rv_KO_CtpD	-0.127	0.241
H37Rv_KO_Rv1272	0.0	0.0
H37Rv_KO_SugABC	0.0	0.099
H37Rv_KO_MbtN	0.334	0.103
Trans05	-0.131	0.0
macrophage_unactivated	0.0	1.708
IL1	0.0	-0.409
Rapamycin	0.0	1.068
Tcell	0.0	0.411
GMCSF	0.0	0.333
IFNab	0.0	0.0
IFNg	0.0	0.0
IFNg_GMCSF1	0.0	0.0
Rv1432_day32	0.0	-0.494
Rv1565c_day32	0.0	0.0
secA2_input	2.113	1.841
delta_Rv3594	1.319	2.49
delta_Rv3717	2.748	1.995
delta_Rv3811	0.518	2.005
delta_Rv0954	0.0	0.917
PonA1	0.0	0.0
EccD1_KO	-0.793	0.0
EspI_KO	0.588	1.292
PE35_KO	0.601	4.238
PPE68_KO	1.238	2.109
glycerol2	-1.307	-1.312
lignocerate	-1.303	-2.604
oleate	-1.517	-3.031
phosphatidylcholine	-1.499	-2.994
acetate	-1.15	0.106
glucAc	-1.106	0.0
Rv0950ko	-0.247	0.172
Rv1096ko	0.0	-0.555
Rv3684ko	2.718	0.701
delta_otsA_trehalose	0.857	-0.096