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 Rv3680/-:

update plot	correlation	link to info on gene
Rv3679/-	(cc=0.6755)	info on Rv3679/-
Rv0505c/serB1	(cc=0.6554)	info on Rv0505c/serB1
Rv1421/-	(cc=0.6354)	info on Rv1421/-
Rv2837c/-	(cc=0.6279)	info on Rv2837c/-
Rv3215/entC	(cc=0.5995)	info on Rv3215/entC
Rv0998/-	(cc=0.5957)	info on Rv0998/-
Rv2966c/-	(cc=0.5688)	info on Rv2966c/-
Rv1821/secA2	(cc=0.5413)	info on Rv1821/secA2
Rv2553c/-	(cc=0.5391)	info on Rv2553c/-
Rv1856c/-	(cc=0.524)	info on Rv1856c/-

Correlation of Rv3680/- with Rv2553c/-

Normalized LFCs for Rv3680/-:
(description and provenance of datasets)

	Rv3680/-	Rv2553c/-
Fe_supp_jason_reseq	1.689	3.321
low_pH_jason_reseq	1.673	0.0
NO_jason_reseq	0.0	0.0
B6_jason_reseq	0.0	0.0
MHCII_jason_reseq	0.0	0.0
Isoniazid02	-1.072	-0.965
Rifampicin4	-0.474	-1.795
Ethambutol3	-0.59	-0.958
Meropenem3	-0.21	0.0
Vancomycin16	-0.464	-2.457
Rv2680_day32	0.0	0.0
H37Rv_KO_MarP	-0.766	-6.0
hypoxia_3wks	-0.55	-0.55
hypoxia_6wks	-0.288	-0.288
glycerol	2.455	0.0
cholesterol	1.612	0.145
AJ	0.0	0.0
Bibs02	1.015	0.0
Bibs02c	1.822	0.0
BL6	0.0	0.0
BL6a	1.812	0.198
BXD01	0.358	0.0
BXD010	0.128	0.0
BXD011	1.109	0.243
BXD03	0.75	0.0
BXD04	0.34	0.0
BXD05	0.369	0.369
BXD06	1.035	0.0
BXD07	0.38	0.0
BXD08	0.253	0.0
BXD09	0.69	0.0
CAST	0.0	0.0
CCcont	1.765	2.448
DS01	0.83	0.0
DS02	0.217	0.0
DS04	1.301	0.682
DS0c	0.413	0.0
GP01	0.0	0.0
GP02	0.0	0.0
GP0c	0.0	0.0
NOD	0.0	0.0
NZO	0.0	0.0
PWK	0.0	0.0
H37Rv_KO_CtpC	0.162	0.162
H37Rv_KO_CtpD	0.445	0.445
H37Rv_KO_Rv1272	0.0	0.0
H37Rv_KO_SugABC	0.768	0.42
H37Rv_KO_MbtN	0.691	0.987
Trans05	0.0	0.131
macrophage_unactivated	0.436	0.0
IL1	0.0	-0.715
Rapamycin	0.0	-0.74
Tcell	0.857	-0.785
GMCSF	0.0	-1.001
IFNab	0.0	0.323
IFNg	0.0	-0.644
IFNg_GMCSF1	0.0	-0.361
Rv1432_day32	0.0	0.0
Rv1565c_day32	0.0	0.0
secA2_input	-2.069	-1.825
delta_Rv3594	1.895	2.723
delta_Rv3717	3.237	3.292
delta_Rv3811	2.787	1.578
delta_Rv0954	0.375	-0.797
PonA1	1.599	0.921
EccD1_KO	0.635	-0.51
EspI_KO	0.878	-1.101
PE35_KO	0.735	-1.476
PPE68_KO	1.245	-0.602
glycerol2	-0.193	-0.68
lignocerate	-0.168	-0.591
oleate	-0.196	-0.688
phosphatidylcholine	-0.193	-0.679
acetate	0.743	-0.806
glucAc	0.462	-0.501
Rv0950ko	-1.9	-6.0
Rv1096ko	-2.111	-0.042
Rv3684ko	-2.663	1.166
delta_otsA_trehalose	0.895	-0.917