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 Rv3208/-:

update plot	correlation	link to info on gene
Rv0955/-	(cc=0.6447)	info on Rv0955/-
Rv0637/hadC	(cc=0.6115)	info on Rv0637/hadC
Rv0489/gpm1	(cc=0.6022)	info on Rv0489/gpm1
Rv3489/-	(cc=0.5782)	info on Rv3489/-
Rv2221c/glnE	(cc=0.5758)	info on Rv2221c/glnE
Rv2678c/hemE	(cc=0.5631)	info on Rv2678c/hemE
Rv3918c/parA	(cc=0.5424)	info on Rv3918c/parA
Rv3753c/-	(cc=0.5422)	info on Rv3753c/-
Rv1565c/-	(cc=0.5311)	info on Rv1565c/-
Rv2553c/-	(cc=0.5213)	info on Rv2553c/-

Correlation of Rv3208/- with Rv1565c/-

Normalized LFCs for Rv3208/-:
(description and provenance of datasets)

	Rv3208/-	Rv1565c/-
Fe_supp_jason_reseq	4.191	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	0.0	-0.383
Rifampicin4	0.0	-0.523
Ethambutol3	0.0	-0.946
Meropenem3	0.0	0.926
Vancomycin16	0.0	-2.064
Rv2680_day32	0.0	0.413
H37Rv_KO_MarP	-1.705	-6.0
hypoxia_3wks	-0.55	-0.885
hypoxia_6wks	-0.288	-0.727
glycerol	0.0	-0.168
cholesterol	0.0	-0.398
AJ	0.0	-0.637
Bibs02	0.0	-0.319
Bibs02c	0.0	-0.365
BL6	0.768	0.351
BL6a	0.0	0.555
BXD01	0.0	0.365
BXD010	0.352	0.0
BXD011	0.35	0.759
BXD03	0.0	0.0
BXD04	0.0	0.49
BXD05	0.135	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	1.43	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	0.357	-0.108
NOD	0.0	-0.392
NZO	0.0	-0.548
PWK	0.0	-0.539
H37Rv_KO_CtpC	0.0	0.968
H37Rv_KO_CtpD	0.0	0.355
H37Rv_KO_Rv1272	0.141	1.542
H37Rv_KO_SugABC	0.348	0.995
H37Rv_KO_MbtN	0.196	1.407
Trans05	0.131	0.195
macrophage_unactivated	0.398	-0.83
IL1	0.374	-1.391
Rapamycin	1.068	-1.439
Tcell	0.0	-0.554
GMCSF	0.333	0.0
IFNab	0.729	-0.248
IFNg	0.93	0.208
IFNg_GMCSF1	0.396	-0.258
Rv1432_day32	0.0	-1.374
Rv1565c_day32	0.0	0.0
secA2_input	-1.368	-3.58
delta_Rv3594	1.487	1.184
delta_Rv3717	1.223	1.019
delta_Rv3811	-0.171	0.546
delta_Rv0954	-0.149	-0.389
PonA1	-0.204	-3.057
EccD1_KO	-1.204	-0.224
EspI_KO	0.0	-0.023
PE35_KO	-2.981	-1.718
PPE68_KO	-2.742	-0.275
glycerol2	-0.82	0.369
lignocerate	-0.712	0.462
oleate	-0.829	0.0
phosphatidylcholine	-0.819	0.193
acetate	-0.973	1.273
glucAc	-0.605	0.877
Rv0950ko	0.311	-2.741
Rv1096ko	-0.513	-2.379
Rv3684ko	0.17	-0.043
delta_otsA_trehalose	0.0	-0.479