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 Rv1669/-:

update plot	correlation	link to info on gene
Rv3839/-	(cc=0.444)	info on Rv3839/-
Rv2352c/PPE38	(cc=0.4404)	info on Rv2352c/PPE38
Rv3438/-	(cc=0.4334)	info on Rv3438/-
Rv2162c/PE_PGRS38	(cc=0.3833)	info on Rv2162c/PE_PGRS38
Rv2973c/recG	(cc=0.3768)	info on Rv2973c/recG
Rv1563c/treY	(cc=0.372)	info on Rv1563c/treY
Rv1562c/treZ	(cc=0.364)	info on Rv1562c/treZ
Rv0255c/cobQ1	(cc=0.3627)	info on Rv0255c/cobQ1
Rv0423c/thiC	(cc=0.3537)	info on Rv0423c/thiC
Rv3742c/-	(cc=0.3512)	info on Rv3742c/-

Correlation of Rv1669/- with Rv1562c/treZ

Normalized LFCs for Rv1669/-:
(description and provenance of datasets)

	Rv1669/-	Rv1562c/treZ
Fe_supp_jason_reseq	0.824	0.761
low_pH_jason_reseq	-0.519	0.773
NO_jason_reseq	-1.756	-0.882
B6_jason_reseq	0.0	-0.093
MHCII_jason_reseq	-0.421	0.508
Isoniazid02	0.167	0.937
Rifampicin4	-0.065	0.236
Ethambutol3	-0.153	0.036
Meropenem3	-0.151	0.036
Vancomycin16	0.804	0.791
Rv2680_day32	0.633	0.321
H37Rv_KO_MarP	-0.601	-0.035
hypoxia_3wks	0.299	-0.478
hypoxia_6wks	-1.969	0.288
glycerol	0.142	-0.771
cholesterol	0.748	0.281
AJ	0.067	0.61
Bibs02	-0.38	-0.121
Bibs02c	1.391	0.717
BL6	-0.45	0.865
BL6a	0.821	0.739
BXD01	-0.204	-0.382
BXD010	-0.137	-0.34
BXD011	1.278	0.0
BXD03	-0.06	0.421
BXD04	0.0	0.077
BXD05	0.884	0.599
BXD06	0.677	0.981
BXD07	0.257	-0.03
BXD08	-0.164	0.135
BXD09	0.407	0.247
CAST	0.591	0.993
CCcont	0.164	1.098
DS01	1.09	0.541
DS02	-0.233	-0.518
DS04	1.681	1.694
DS0c	0.267	0.178
GP01	-0.508	0.683
GP02	0.547	0.162
GP0c	0.177	0.465
NOD	0.576	0.047
NZO	0.621	-0.475
PWK	0.524	1.056
H37Rv_KO_CtpC	-0.76	0.653
H37Rv_KO_CtpD	0.173	0.053
H37Rv_KO_Rv1272	1.483	-0.192
H37Rv_KO_SugABC	0.029	0.663
H37Rv_KO_MbtN	-0.214	0.965
Trans05	1.157	-0.057
macrophage_unactivated	1.035	-0.076
IL1	-0.042	0.068
Rapamycin	-0.703	-0.457
Tcell	-0.433	0.0
GMCSF	0.895	-0.325
IFNab	0.33	-0.145
IFNg	0.462	-0.329
IFNg_GMCSF1	1.169	0.148
Rv1432_day32	0.074	0.222
Rv1565c_day32	0.444	0.458
secA2_input	-0.171	-0.153
delta_Rv3594	0.0	-0.087
delta_Rv3717	-0.287	0.378
delta_Rv3811	0.611	0.08
delta_Rv0954	-0.093	-0.036
PonA1	0.02	0.876
EccD1_KO	-0.566	0.322
EspI_KO	-0.73	0.071
PE35_KO	-0.16	1.155
PPE68_KO	1.075	0.534
glycerol2	-0.559	0.736
lignocerate	-0.296	1.084
oleate	-0.345	-1.012
phosphatidylcholine	-0.071	0.556
acetate	0.346	1.416
glucAc	-0.08	1.459
Rv0950ko	0.766	-0.238
Rv1096ko	0.856	-0.829
Rv3684ko	-0.187	-0.75
delta_otsA_trehalose	2.546	5.496