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 Rv3373/echA18:

update plot	correlation	link to info on gene
Rv0691c/-	(cc=0.4411)	info on Rv0691c/-
Rv3626c/-	(cc=0.3899)	info on Rv3626c/-
Rv0778/cyp126	(cc=0.3752)	info on Rv0778/cyp126
Rv0146/-	(cc=0.3708)	info on Rv0146/-
Rv0300/vapB2	(cc=0.3696)	info on Rv0300/vapB2
Rv1261c/-	(cc=0.3689)	info on Rv1261c/-
Rv3452/cut4	(cc=0.3634)	info on Rv3452/cut4
Rv0463/-	(cc=0.3626)	info on Rv0463/-
Rv1574/-	(cc=0.3608)	info on Rv1574/-
Rv3741c/-	(cc=0.3605)	info on Rv3741c/-

Correlation of Rv3373/echA18 with Rv0778/cyp126

Normalized LFCs for Rv3373/echA18:
(description and provenance of datasets)

	Rv3373/echA18	Rv0778/cyp126
Fe_supp_jason_reseq	1.089	2.014
low_pH_jason_reseq	-2.466	-0.571
NO_jason_reseq	0.475	-0.651
B6_jason_reseq	-1.006	0.523
MHCII_jason_reseq	-0.077	0.706
Isoniazid02	0.303	-0.525
Rifampicin4	-1.021	0.157
Ethambutol3	-0.269	-0.403
Meropenem3	2.485	0.298
Vancomycin16	0.202	0.154
Rv2680_day32	0.499	0.508
H37Rv_KO_MarP	-1.851	-0.423
hypoxia_3wks	0.475	0.534
hypoxia_6wks	-0.954	-0.021
glycerol	-0.211	0.736
cholesterol	1.444	0.449
AJ	1.914	0.824
Bibs02	1.057	0.174
Bibs02c	0.077	0.246
BL6	0.104	-0.148
BL6a	0.722	0.756
BXD01	1.038	0.734
BXD010	-1.92	0.959
BXD011	-0.281	0.899
BXD03	0.232	0.561
BXD04	0.406	1.184
BXD05	0.216	0.862
BXD06	-0.139	0.836
BXD07	0.517	0.79
BXD08	0.228	0.618
BXD09	0.133	0.696
CAST	0.561	0.756
CCcont	0.037	-0.056
DS01	0.575	0.921
DS02	-0.69	1.078
DS04	-0.489	0.207
DS0c	-0.878	0.919
GP01	-1.711	-0.265
GP02	-1.623	-0.021
GP0c	-0.818	0.665
NOD	-1.572	1.642
NZO	0.445	0.581
PWK	-0.831	0.715
H37Rv_KO_CtpC	-0.384	0.916
H37Rv_KO_CtpD	2.245	1.194
H37Rv_KO_Rv1272	-1.619	-0.269
H37Rv_KO_SugABC	-0.877	1.345
H37Rv_KO_MbtN	1.805	0.918
Trans05	-1.195	0.278
macrophage_unactivated	-0.218	1.042
IL1	-0.05	0.0
Rapamycin	0.534	0.341
Tcell	0.518	0.437
GMCSF	0.536	0.591
IFNab	-0.369	0.0
IFNg	1.088	1.04
IFNg_GMCSF1	-0.053	0.566
Rv1432_day32	-2.327	-0.624
Rv1565c_day32	-1.802	-0.347
secA2_input	-2.264	0.23
delta_Rv3594	-1.092	0.72
delta_Rv3717	-3.62	-0.162
delta_Rv3811	-0.922	0.744
delta_Rv0954	-0.751	0.549
PonA1	0.048	0.753
EccD1_KO	0.178	0.52
EspI_KO	0.65	0.893
PE35_KO	0.866	0.983
PPE68_KO	-0.71	0.841
glycerol2	0.129	-0.13
lignocerate	-0.304	-0.614
oleate	0.658	0.39
phosphatidylcholine	0.231	0.088
acetate	0.54	-0.748
glucAc	-0.923	-1.202
Rv0950ko	0.887	0.329
Rv1096ko	1.457	0.633
Rv3684ko	0.92	0.121
delta_otsA_trehalose	-2.912	-1.184