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 Rv3618/-:

update plot	correlation	link to info on gene
Rv3786c/-	(cc=0.573)	info on Rv3786c/-
Rv0312/-	(cc=0.5)	info on Rv0312/-
Rv1062/-	(cc=0.4966)	info on Rv1062/-
Rv2813/-	(cc=0.4937)	info on Rv2813/-
Rv3335c/-	(cc=0.4756)	info on Rv3335c/-
Rv0060/-	(cc=0.4688)	info on Rv0060/-
Rv3428c/-	(cc=0.4632)	info on Rv3428c/-
Rv2237/-	(cc=0.455)	info on Rv2237/-
Rv0445c/sigK	(cc=0.4529)	info on Rv0445c/sigK
Rv3703c/-	(cc=0.4512)	info on Rv3703c/-

Correlation of Rv3618/- with Rv0060/-

Normalized LFCs for Rv3618/-:
(description and provenance of datasets)

	Rv3618/-	Rv0060/-
Fe_supp_jason_reseq	-0.065	0.391
low_pH_jason_reseq	-0.505	-1.134
NO_jason_reseq	-0.053	0.0
B6_jason_reseq	-0.153	0.0
MHCII_jason_reseq	0.652	0.085
Isoniazid02	0.0	0.263
Rifampicin4	-0.485	0.712
Ethambutol3	-0.033	0.505
Meropenem3	-0.065	0.662
Vancomycin16	-0.096	0.48
Rv2680_day32	-0.956	-0.554
H37Rv_KO_MarP	0.04	0.35
hypoxia_3wks	-0.355	-0.606
hypoxia_6wks	-0.405	0.146
glycerol	0.209	0.222
cholesterol	0.377	0.0
AJ	0.435	0.131
Bibs02	-0.538	-1.123
Bibs02c	-0.271	0.629
BL6	0.362	0.53
BL6a	0.026	0.595
BXD01	-0.217	0.905
BXD010	-0.334	-0.543
BXD011	0.064	0.268
BXD03	0.068	0.52
BXD04	-0.244	-0.325
BXD05	0.459	0.216
BXD06	-0.163	0.342
BXD07	-0.027	0.0
BXD08	-0.262	0.0
BXD09	0.07	-0.173
CAST	0.185	0.976
CCcont	0.129	1.498
DS01	-0.394	-0.45
DS02	0.187	1.235
DS04	-0.142	0.312
DS0c	-0.234	-0.737
GP01	-0.233	0.056
GP02	-0.47	-0.283
GP0c	-0.777	0.942
NOD	1.699	0.0
NZO	0.416	0.6
PWK	0.388	0.905
H37Rv_KO_CtpC	-0.234	0.977
H37Rv_KO_CtpD	-0.26	0.989
H37Rv_KO_Rv1272	-0.579	0.227
H37Rv_KO_SugABC	1.365	0.877
H37Rv_KO_MbtN	0.154	-0.633
Trans05	-0.104	-0.554
macrophage_unactivated	-0.287	1.531
IL1	-0.424	-0.297
Rapamycin	0.399	0.0
Tcell	-0.033	1.352
GMCSF	0.594	-0.264
IFNab	-0.151	0.0
IFNg	0.128	-0.551
IFNg_GMCSF1	0.886	-0.314
Rv1432_day32	0.12	0.0
Rv1565c_day32	-1.06	-0.218
secA2_input	0.618	0.812
delta_Rv3594	0.471	0.961
delta_Rv3717	0.513	1.851
delta_Rv3811	0.7	1.335
delta_Rv0954	0.072	0.0
PonA1	0.42	-0.245
EccD1_KO	-0.237	0.582
EspI_KO	-0.827	-0.787
PE35_KO	-0.053	-0.589
PPE68_KO	0.0	-1.133
glycerol2	0.891	1.964
lignocerate	1.001	2.404
oleate	-0.231	-0.688
phosphatidylcholine	0.913	1.909
acetate	1.084	2.128
glucAc	1.245	1.868
Rv0950ko	0.691	0.639
Rv1096ko	0.283	1.194
Rv3684ko	0.658	0.0
delta_otsA_trehalose	0.168	0.366