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 Rv0076c/-:

update plot	correlation	link to info on gene
Rv2430c/PPE41	(cc=0.5092)	info on Rv2430c/PPE41
Rv0805/-	(cc=0.4827)	info on Rv0805/-
Rv2501c/accA1	(cc=0.4776)	info on Rv2501c/accA1
Rv0762c/-	(cc=0.4763)	info on Rv0762c/-
Rv1169c/lipX	(cc=0.4717)	info on Rv1169c/lipX
Rv3278c/-	(cc=0.4694)	info on Rv3278c/-
Rv0371c/-	(cc=0.4611)	info on Rv0371c/-
Rv3528c/-	(cc=0.461)	info on Rv3528c/-
Rv1051c/-	(cc=0.4598)	info on Rv1051c/-
Rv0742/PE_PGRS8	(cc=0.458)	info on Rv0742/PE_PGRS8

Correlation of Rv0076c/- with Rv2501c/accA1

Normalized LFCs for Rv0076c/-:
(description and provenance of datasets)

	Rv0076c/-	Rv2501c/accA1
Fe_supp_jason_reseq	-0.559	-0.052
low_pH_jason_reseq	0.234	-0.622
NO_jason_reseq	-2.184	0.168
B6_jason_reseq	-0.605	-1.11
MHCII_jason_reseq	-0.346	-0.323
Isoniazid02	-1.0	-1.455
Rifampicin4	0.799	1.045
Ethambutol3	-0.209	-0.814
Meropenem3	-0.615	-0.801
Vancomycin16	-0.106	-0.39
Rv2680_day32	-0.077	-1.015
H37Rv_KO_MarP	0.817	0.178
hypoxia_3wks	-0.064	-0.478
hypoxia_6wks	-0.524	-0.251
glycerol	-0.471	0.256
cholesterol	0.395	0.597
AJ	0.091	0.904
Bibs02	0.481	0.58
Bibs02c	-0.073	0.202
BL6	0.653	0.651
BL6a	0.64	1.187
BXD01	0.973	0.38
BXD010	2.436	0.928
BXD011	0.814	0.834
BXD03	1.385	1.409
BXD04	0.041	2.038
BXD05	0.68	1.385
BXD06	1.004	0.775
BXD07	0.979	0.256
BXD08	0.929	0.169
BXD09	1.404	1.018
CAST	0.963	-0.078
CCcont	1.571	1.107
DS01	0.811	-0.08
DS02	1.741	0.58
DS04	3.287	0.843
DS0c	0.503	-0.313
GP01	-0.396	0.182
GP02	0.875	1.155
GP0c	1.028	0.0
NOD	0.753	0.926
NZO	1.123	0.532
PWK	0.61	0.249
H37Rv_KO_CtpC	1.058	1.309
H37Rv_KO_CtpD	-1.286	1.664
H37Rv_KO_Rv1272	1.515	0.179
H37Rv_KO_SugABC	-0.183	-0.751
H37Rv_KO_MbtN	0.643	-0.072
Trans05	1.004	0.166
macrophage_unactivated	2.153	0.915
IL1	-0.077	0.451
Rapamycin	0.012	0.654
Tcell	0.603	-0.228
GMCSF	-0.457	0.911
IFNab	0.012	0.203
IFNg	1.211	0.238
IFNg_GMCSF1	0.261	0.0
Rv1432_day32	0.691	1.025
Rv1565c_day32	-1.194	-1.549
secA2_input	0.773	0.831
delta_Rv3594	-1.227	-0.667
delta_Rv3717	-1.034	-0.347
delta_Rv3811	-1.478	-0.354
delta_Rv0954	-0.972	-0.406
PonA1	-0.891	-0.362
EccD1_KO	-0.322	-0.595
EspI_KO	-0.876	-0.425
PE35_KO	-0.12	0.16
PPE68_KO	-0.611	-0.278
glycerol2	-0.008	-0.045
lignocerate	0.253	0.407
oleate	-0.021	-0.138
phosphatidylcholine	-0.091	0.324
acetate	-0.199	0.384
glucAc	2.151	0.267
Rv0950ko	0.154	0.356
Rv1096ko	-0.594	0.914
Rv3684ko	0.2	0.098
delta_otsA_trehalose	0.183	0.238