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 Rv2553c/-:

update plot	correlation	link to info on gene
Rv1836c/-	(cc=0.8859)	info on Rv1836c/-
Rv3102c/ftsE	(cc=0.8112)	info on Rv3102c/ftsE
Rv3101c/ftsX	(cc=0.7945)	info on Rv3101c/ftsX
Rv3671c/-	(cc=0.7418)	info on Rv3671c/-
Rv2837c/-	(cc=0.7308)	info on Rv2837c/-
Rv1565c/-	(cc=0.7196)	info on Rv1565c/-
Rv1821/secA2	(cc=0.6983)	info on Rv1821/secA2
Rv3593/lpqF	(cc=0.6952)	info on Rv3593/lpqF
Rv2190c/-	(cc=0.6903)	info on Rv2190c/-
Rv1080c/greA	(cc=0.6866)	info on Rv1080c/greA

Correlation of Rv2553c/- with Rv1565c/-

Normalized LFCs for Rv2553c/-:
(description and provenance of datasets)

	Rv2553c/-	Rv1565c/-
Fe_supp_jason_reseq	3.321	4.537
low_pH_jason_reseq	0.0	0.156
NO_jason_reseq	0.0	0.475
B6_jason_reseq	0.0	0.881
MHCII_jason_reseq	0.0	0.603
Isoniazid02	-0.965	-0.383
Rifampicin4	-1.795	-0.523
Ethambutol3	-0.958	-0.946
Meropenem3	0.0	0.926
Vancomycin16	-2.457	-2.064
Rv2680_day32	0.0	0.413
H37Rv_KO_MarP	-6.0	-6.0
hypoxia_3wks	-0.55	-0.885
hypoxia_6wks	-0.288	-0.727
glycerol	0.0	-0.168
cholesterol	0.145	-0.398
AJ	0.0	-0.637
Bibs02	0.0	-0.319
Bibs02c	0.0	-0.365
BL6	0.0	0.351
BL6a	0.198	0.555
BXD01	0.0	0.365
BXD010	0.0	0.0
BXD011	0.243	0.759
BXD03	0.0	0.0
BXD04	0.0	0.49
BXD05	0.369	0.533
BXD06	0.0	-0.111
BXD07	0.0	0.0
BXD08	0.0	0.103
BXD09	0.0	0.109
CAST	0.0	-0.632
CCcont	2.448	2.714
DS01	0.0	-0.648
DS02	0.0	-0.597
DS04	0.682	1.244
DS0c	0.0	-0.596
GP01	0.0	-0.271
GP02	0.0	-0.228
GP0c	0.0	-0.108
NOD	0.0	-0.392
NZO	0.0	-0.548
PWK	0.0	-0.539
H37Rv_KO_CtpC	0.162	0.968
H37Rv_KO_CtpD	0.445	0.355
H37Rv_KO_Rv1272	0.0	1.542
H37Rv_KO_SugABC	0.42	0.995
H37Rv_KO_MbtN	0.987	1.407
Trans05	0.131	0.195
macrophage_unactivated	0.0	-0.83
IL1	-0.715	-1.391
Rapamycin	-0.74	-1.439
Tcell	-0.785	-0.554
GMCSF	-1.001	0.0
IFNab	0.323	-0.248
IFNg	-0.644	0.208
IFNg_GMCSF1	-0.361	-0.258
Rv1432_day32	0.0	-1.374
Rv1565c_day32	0.0	0.0
secA2_input	-1.825	-3.58
delta_Rv3594	2.723	1.184
delta_Rv3717	3.292	1.019
delta_Rv3811	1.578	0.546
delta_Rv0954	-0.797	-0.389
PonA1	0.921	-3.057
EccD1_KO	-0.51	-0.224
EspI_KO	-1.101	-0.023
PE35_KO	-1.476	-1.718
PPE68_KO	-0.602	-0.275
glycerol2	-0.68	0.369
lignocerate	-0.591	0.462
oleate	-0.688	0.0
phosphatidylcholine	-0.679	0.193
acetate	-0.806	1.273
glucAc	-0.501	0.877
Rv0950ko	-6.0	-2.741
Rv1096ko	-0.042	-2.379
Rv3684ko	1.166	-0.043
delta_otsA_trehalose	-0.917	-0.479