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 Rv3098A/-:

update plot	correlation	link to info on gene
Rv2355/-	(cc=0.591)	info on Rv2355/-
Rv3187/-	(cc=0.5517)	info on Rv3187/-
Rv1756c/-	(cc=0.5514)	info on Rv1756c/-
Rv2649/-	(cc=0.5476)	info on Rv2649/-
Rv2167c/-	(cc=0.5384)	info on Rv2167c/-
Rv2106/-	(cc=0.5355)	info on Rv2106/-
Rv2479c/-	(cc=0.533)	info on Rv2479c/-
Rv2279/-	(cc=0.5313)	info on Rv2279/-
Rv1764/-	(cc=0.5268)	info on Rv1764/-
Rv3380c/-	(cc=0.5241)	info on Rv3380c/-

Correlation of Rv3098A/- with Rv2355/-

Normalized LFCs for Rv3098A/-:
(description and provenance of datasets)

	Rv3098A/-	Rv2355/-
Fe_supp_jason_reseq	0.044	0.044
low_pH_jason_reseq	-1.188	-0.564
NO_jason_reseq	0.142	0.158
B6_jason_reseq	0.385	-0.298
MHCII_jason_reseq	0.266	0.054
Isoniazid02	-0.405	0.047
Rifampicin4	-0.298	1.018
Ethambutol3	0.265	0.416
Meropenem3	-0.454	-0.135
Vancomycin16	-0.355	0.013
Rv2680_day32	-0.694	-0.084
H37Rv_KO_MarP	-0.063	-0.285
hypoxia_3wks	0.223	0.419
hypoxia_6wks	0.207	0.125
glycerol	0.478	-0.866
cholesterol	0.395	-0.016
AJ	0.202	1.197
Bibs02	0.276	1.068
Bibs02c	1.188	1.675
BL6	0.634	0.217
BL6a	0.574	1.072
BXD01	-0.43	0.643
BXD010	0.611	0.786
BXD011	0.249	0.752
BXD03	-0.117	0.715
BXD04	0.009	0.455
BXD05	0.363	0.947
BXD06	-0.017	0.431
BXD07	-0.232	0.655
BXD08	-0.372	0.538
BXD09	0.142	0.65
CAST	0.799	1.089
CCcont	0.119	0.177
DS01	0.226	0.972
DS02	0.255	1.007
DS04	0.43	1.317
DS0c	0.338	1.042
GP01	0.159	1.034
GP02	0.4	1.191
GP0c	-0.232	0.53
NOD	1.832	1.318
NZO	0.665	0.984
PWK	0.642	1.098
H37Rv_KO_CtpC	0.514	0.752
H37Rv_KO_CtpD	0.101	0.953
H37Rv_KO_Rv1272	1.072	0.57
H37Rv_KO_SugABC	0.372	1.016
H37Rv_KO_MbtN	0.751	0.685
Trans05	1.137	0.851
macrophage_unactivated	-0.881	-0.59
IL1	-0.139	-0.306
Rapamycin	0.015	-0.335
Tcell	-0.049	-1.017
GMCSF	0.409	-0.272
IFNab	-0.457	-0.729
IFNg	-0.12	-0.428
IFNg_GMCSF1	0.189	-0.226
Rv1432_day32	0.58	0.492
Rv1565c_day32	-0.453	0.278
secA2_input	-0.888	-0.315
delta_Rv3594	-0.3	-0.153
delta_Rv3717	-0.243	-0.344
delta_Rv3811	-0.9	-0.116
delta_Rv0954	-0.089	0.429
PonA1	-0.383	0.0
EccD1_KO	0.115	0.214
EspI_KO	0.083	0.676
PE35_KO	0.601	0.79
PPE68_KO	0.445	0.464
glycerol2	-0.261	-0.787
lignocerate	0.302	-0.553
oleate	-1.053	-0.871
phosphatidylcholine	-0.118	-0.774
acetate	-0.851	-0.321
glucAc	-0.213	-0.055
Rv0950ko	0.724	0.166
Rv1096ko	-0.232	-0.018
Rv3684ko	-0.557	-0.38
delta_otsA_trehalose	-0.41	-0.173