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 Rv3415c/-:

update plot	correlation	link to info on gene
Rv2695/-	(cc=0.3925)	info on Rv2695/-
Rv1489/-	(cc=0.3917)	info on Rv1489/-
Rv3158/nuoN	(cc=0.3853)	info on Rv3158/nuoN
Rv1004c/-	(cc=0.3795)	info on Rv1004c/-
Rv0021c/-	(cc=0.3718)	info on Rv0021c/-
Rv1191/-	(cc=0.3718)	info on Rv1191/-
Rv3297/nei	(cc=0.361)	info on Rv3297/nei
Rv2801c/mazF9	(cc=0.3604)	info on Rv2801c/mazF9
Rv2769c/PE27	(cc=0.359)	info on Rv2769c/PE27
Rv0279c/PE_PGRS4	(cc=0.3578)	info on Rv0279c/PE_PGRS4

Correlation of Rv3415c/- with Rv2695/-

Normalized LFCs for Rv3415c/-:
(description and provenance of datasets)

	Rv3415c/-	Rv2695/-
Fe_supp_jason_reseq	0.248	0.0
low_pH_jason_reseq	-0.547	-0.8
NO_jason_reseq	0.176	0.711
B6_jason_reseq	-0.869	-0.11
MHCII_jason_reseq	0.01	0.544
Isoniazid02	0.597	0.664
Rifampicin4	1.032	0.799
Ethambutol3	0.761	0.759
Meropenem3	1.618	0.167
Vancomycin16	1.051	0.074
Rv2680_day32	1.325	1.658
H37Rv_KO_MarP	0.928	-0.137
hypoxia_3wks	0.211	0.0
hypoxia_6wks	0.157	0.85
glycerol	0.932	-0.098
cholesterol	-0.142	0.328
AJ	-0.067	1.126
Bibs02	1.298	1.22
Bibs02c	0.267	0.527
BL6	-0.122	0.703
BL6a	0.762	0.743
BXD01	0.877	1.038
BXD010	-0.198	0.948
BXD011	0.045	0.722
BXD03	0.955	0.514
BXD04	0.982	0.342
BXD05	1.108	1.327
BXD06	0.047	0.224
BXD07	0.725	0.771
BXD08	0.736	1.103
BXD09	0.433	0.479
CAST	0.175	0.053
CCcont	0.2	0.178
DS01	1.122	1.935
DS02	1.711	1.531
DS04	0.424	2.09
DS0c	0.525	0.965
GP01	0.705	2.283
GP02	0.591	2.524
GP0c	0.624	2.06
NOD	-0.309	-0.146
NZO	0.318	0.704
PWK	0.082	0.432
H37Rv_KO_CtpC	-1.626	1.098
H37Rv_KO_CtpD	-0.918	0.851
H37Rv_KO_Rv1272	0.834	1.466
H37Rv_KO_SugABC	0.461	1.415
H37Rv_KO_MbtN	-0.101	1.95
Trans05	1.142	1.609
macrophage_unactivated	-0.066	0.366
IL1	0.125	1.038
Rapamycin	0.169	1.04
Tcell	0.0	0.358
GMCSF	-0.309	-0.071
IFNab	-0.641	-0.039
IFNg	-0.438	-0.861
IFNg_GMCSF1	0.0	0.167
Rv1432_day32	0.446	2.315
Rv1565c_day32	-0.842	-0.531
secA2_input	-0.056	-0.495
delta_Rv3594	0.167	-0.424
delta_Rv3717	-0.278	-0.293
delta_Rv3811	0.428	-0.958
delta_Rv0954	0.597	-0.603
PonA1	0.263	-1.173
EccD1_KO	0.056	0.681
EspI_KO	-0.145	0.08
PE35_KO	-0.018	0.379
PPE68_KO	-0.275	0.397
glycerol2	0.859	-0.577
lignocerate	0.012	-0.828
oleate	0.267	-0.478
phosphatidylcholine	-1.209	-2.76
acetate	0.924	-0.771
glucAc	-0.113	-0.837
Rv0950ko	0.374	0.802
Rv1096ko	0.259	0.365
Rv3684ko	-0.668	0.652
delta_otsA_trehalose	-0.526	-1.39