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 Rv3679/-:
Show top 50 genes. Show bottom 10 genes with LOWEST correlation.

Most correlated genes.

update plot	correlation	link to info on gene
Rv3680/-	(cc=0.6755)	info on Rv3680/-
Rv0989c/grcC2	(cc=0.6014)	info on Rv0989c/grcC2
Rv2190c/-	(cc=0.5824)	info on Rv2190c/-
Rv0017c/rodA	(cc=0.5641)	info on Rv0017c/rodA
Rv1421/-	(cc=0.5619)	info on Rv1421/-
Rv0505c/serB1	(cc=0.5574)	info on Rv0505c/serB1
Rv1745c/idi	(cc=0.5513)	info on Rv1745c/idi
Rv0820/phoT	(cc=0.5484)	info on Rv0820/phoT
Rv0930/pstA1	(cc=0.542)	info on Rv0930/pstA1
Rv0924c/mntH	(cc=0.5365)	info on Rv0924c/mntH

Correlation of Rv3679/- with Rv3680/-

Normalized LFCs for Rv3679/-:
(description and provenance of datasets)

Comparison of LFCs between selected condtions.

condition	Rv3679/-	Rv3680/-
Fe_supp_jason_reseq	1.354	1.689
low_pH_jason_reseq	1.747	1.673
NO_jason_reseq	-1.42	0.0
B6_jason_reseq	-0.752	0.0
MHCII_jason_reseq	1.103	0.0
Isoniazid02	-1.072	-1.072
Rifampicin4	0.252	-0.474
Ethambutol3	-0.297	-0.59
Meropenem3	-0.161	-0.21
Vancomycin16	0.085	-0.464
Rv2680_day32	1.078	0.0
H37Rv_KO_MarP	-0.969	-0.766
hypoxia_3wks	0.0	-0.55
hypoxia_6wks	-0.24	-0.288
glycerol	3.461	2.455
cholesterol	2.365	1.612
AJ	0.0	0.0
Bibs02	1.999	1.015
Bibs02c	2.102	1.822
BL6	1.623	0.0
BL6a	2.108	1.812
BXD01	0.994	0.358
BXD010	2.069	0.128
BXD011	2.333	1.109
BXD03	1.903	0.75
BXD04	0.896	0.34
BXD05	0.919	0.369
BXD06	1.533	1.035
BXD07	1.662	0.38
BXD08	1.016	0.253
BXD09	1.323	0.69
CAST	-0.402	0.0
CCcont	1.867	1.765
DS01	1.803	0.83
DS02	1.297	0.217
DS04	2.228	1.301
DS0c	1.293	0.413
GP01	0.589	0.0
GP02	0.124	0.0
GP0c	2.228	0.0
NOD	1.44	0.0
NZO	-0.548	0.0
PWK	-0.539	0.0
H37Rv_KO_CtpC	0.353	0.162
H37Rv_KO_CtpD	0.865	0.445
H37Rv_KO_Rv1272	-0.246	0.0
H37Rv_KO_SugABC	0.278	0.768
H37Rv_KO_MbtN	0.408	0.691
Trans05	-0.109	0.0
macrophage_unactivated	-0.234	0.436
IL1	-0.694	0.0
Rapamycin	-0.466	0.0
Tcell	-0.241	0.857
GMCSF	-1.096	0.0
IFNab	0.795	0.0
IFNg	-0.198	0.0
IFNg_GMCSF1	-0.478	0.0
Rv1432_day32	0.0	0.0
Rv1565c_day32	0.0	0.0
secA2_input	-3.694	-2.069
delta_Rv3594	1.341	1.895
delta_Rv3717	1.609	3.237
delta_Rv3811	0.995	2.787
delta_Rv0954	-1.739	0.375
PonA1	0.684	1.599
EccD1_KO	0.901	0.635
EspI_KO	-0.063	0.878
PE35_KO	-1.068	0.735
PPE68_KO	-0.745	1.245
glycerol2	-0.193	-0.193
lignocerate	0.153	-0.168
oleate	-0.196	-0.196
phosphatidylcholine	-0.193	-0.193
acetate	0.209	0.743
glucAc	0.891	0.462
Rv0950ko	-1.251	-1.9
Rv1096ko	-1.155	-2.111
Rv3684ko	-1.575	-2.663
delta_otsA_trehalose	2.288	0.895