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 Rv1718/-:

update plot	correlation	link to info on gene
Rv1403c/-	(cc=0.6247)	info on Rv1403c/-
Rv1289/-	(cc=0.6185)	info on Rv1289/-
Rv0089/-	(cc=0.5555)	info on Rv0089/-
Rv0963c/-	(cc=0.5548)	info on Rv0963c/-
Rv0278c/PE_PGRS3	(cc=0.551)	info on Rv0278c/PE_PGRS3
Rv2426c/-	(cc=0.5476)	info on Rv2426c/-
Rv1281c/oppD	(cc=0.5182)	info on Rv1281c/oppD
Rv2919c/glnB	(cc=0.5137)	info on Rv2919c/glnB
Rv3081/-	(cc=0.5097)	info on Rv3081/-
Rv0226c/-	(cc=0.5072)	info on Rv0226c/-

Correlation of Rv1718/- with Rv0089/-

Normalized LFCs for Rv1718/-:
(description and provenance of datasets)

	Rv1718/-	Rv0089/-
Fe_supp_jason_reseq	0.308	-0.617
low_pH_jason_reseq	-0.263	-0.221
NO_jason_reseq	0.441	0.047
B6_jason_reseq	1.117	0.241
MHCII_jason_reseq	0.368	0.487
Isoniazid02	0.017	0.877
Rifampicin4	-0.133	-0.701
Ethambutol3	-0.338	-0.483
Meropenem3	-0.167	-0.564
Vancomycin16	-0.196	0.0
Rv2680_day32	-1.001	1.554
H37Rv_KO_MarP	-0.048	1.943
hypoxia_3wks	-1.105	-0.59
hypoxia_6wks	-0.374	-0.699
glycerol	0.528	-1.188
cholesterol	0.943	-0.61
AJ	-0.264	0.069
Bibs02	1.484	0.098
Bibs02c	0.411	0.0
BL6	-1.198	-1.724
BL6a	-0.349	-1.411
BXD01	-1.54	-1.681
BXD010	0.777	-1.478
BXD011	-1.002	-1.727
BXD03	-1.295	-1.397
BXD04	-0.491	-0.973
BXD05	-1.649	-1.529
BXD06	-0.683	-1.642
BXD07	-0.739	-2.006
BXD08	-0.835	-2.382
BXD09	-0.688	-1.596
CAST	1.111	0.492
CCcont	-0.466	-0.977
DS01	0.941	-0.209
DS02	1.095	0.153
DS04	0.673	0.462
DS0c	1.259	0.308
GP01	0.497	0.326
GP02	0.486	-1.336
GP0c	-0.801	-0.489
NOD	-0.543	0.145
NZO	0.663	-0.1
PWK	-0.361	0.389
H37Rv_KO_CtpC	-0.067	-1.138
H37Rv_KO_CtpD	-0.384	-3.064
H37Rv_KO_Rv1272	-0.415	-0.742
H37Rv_KO_SugABC	-0.273	-0.481
H37Rv_KO_MbtN	-1.666	-1.571
Trans05	0.807	0.008
macrophage_unactivated	-0.761	-2.727
IL1	0.071	-1.246
Rapamycin	-0.436	-2.071
Tcell	-1.447	-1.3
GMCSF	-0.269	-1.848
IFNab	-0.151	-2.524
IFNg	-0.762	-1.871
IFNg_GMCSF1	-0.848	-0.936
Rv1432_day32	-0.185	0.301
Rv1565c_day32	-0.287	0.594
secA2_input	-1.11	-1.028
delta_Rv3594	0.211	0.0
delta_Rv3717	-0.473	-0.216
delta_Rv3811	-0.269	0.755
delta_Rv0954	-1.105	0.442
PonA1	-1.477	-0.308
EccD1_KO	0.289	-0.118
EspI_KO	1.802	1.221
PE35_KO	0.916	0.204
PPE68_KO	0.765	1.497
glycerol2	0.534	1.494
lignocerate	1.818	1.736
oleate	-2.789	-0.505
phosphatidylcholine	0.985	1.304
acetate	2.095	2.168
glucAc	1.951	1.508
Rv0950ko	-0.232	-0.169
Rv1096ko	0.853	0.983
Rv3684ko	0.174	1.019
delta_otsA_trehalose	0.363	1.304