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 Rv3679/-

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

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