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 Rv2456c/-:

update plot	correlation	link to info on gene
Rv1831/-	(cc=0.6179)	info on Rv1831/-
Rv2663/-	(cc=0.5981)	info on Rv2663/-
Rv3689/-	(cc=0.5823)	info on Rv3689/-
Rv2833c/ugpB	(cc=0.5803)	info on Rv2833c/ugpB
Rv1387/PPE20	(cc=0.5712)	info on Rv1387/PPE20
Rv0188/-	(cc=0.5689)	info on Rv0188/-
Rv3210c/-	(cc=0.5684)	info on Rv3210c/-
Rv3842c/glpQ1	(cc=0.562)	info on Rv3842c/glpQ1
Rv2243/fabD	(cc=0.5364)	info on Rv2243/fabD
Rv3148/nuoD	(cc=0.5359)	info on Rv3148/nuoD

Correlation of Rv2456c/- with Rv2663/-

Normalized LFCs for Rv2456c/-:
(description and provenance of datasets)

	Rv2456c/-	Rv2663/-
Fe_supp_jason_reseq	-0.379	-0.313
low_pH_jason_reseq	-1.086	-0.796
NO_jason_reseq	0.0	0.0
B6_jason_reseq	0.476	-0.048
MHCII_jason_reseq	-0.595	-1.328
Isoniazid02	0.215	-1.227
Rifampicin4	0.143	-0.13
Ethambutol3	0.591	0.458
Meropenem3	-0.126	-0.492
Vancomycin16	0.048	-0.748
Rv2680_day32	0.302	0.36
H37Rv_KO_MarP	0.071	-0.859
hypoxia_3wks	-0.423	0.439
hypoxia_6wks	0.355	0.674
glycerol	-0.648	-0.6
cholesterol	0.259	0.335
AJ	-0.224	0.645
Bibs02	-0.301	-0.788
Bibs02c	-0.076	-0.032
BL6	0.922	1.218
BL6a	0.716	0.779
BXD01	0.662	1.227
BXD010	0.612	0.849
BXD011	1.502	0.89
BXD03	0.774	0.578
BXD04	1.111	0.988
BXD05	0.484	0.874
BXD06	0.863	1.333
BXD07	0.971	0.989
BXD08	0.717	1.768
BXD09	0.702	1.427
CAST	0.929	1.538
CCcont	0.332	0.567
DS01	-0.399	-0.734
DS02	0.0	-0.35
DS04	-0.128	0.122
DS0c	0.061	-0.644
GP01	0.393	0.378
GP02	0.291	-0.328
GP0c	0.461	0.635
NOD	0.428	0.244
NZO	0.321	0.262
PWK	0.186	0.745
H37Rv_KO_CtpC	0.495	0.401
H37Rv_KO_CtpD	-0.268	1.363
H37Rv_KO_Rv1272	0.562	1.409
H37Rv_KO_SugABC	-0.214	-0.159
H37Rv_KO_MbtN	0.886	-0.279
Trans05	1.071	1.534
macrophage_unactivated	-0.167	0.028
IL1	0.077	0.86
Rapamycin	-0.009	-0.114
Tcell	0.502	1.004
GMCSF	0.185	0.082
IFNab	-0.212	0.027
IFNg	0.195	0.235
IFNg_GMCSF1	0.031	0.434
Rv1432_day32	0.149	0.495
Rv1565c_day32	-0.442	0.474
secA2_input	-0.092	0.29
delta_Rv3594	0.138	-0.389
delta_Rv3717	0.457	0.357
delta_Rv3811	-0.303	-0.724
delta_Rv0954	-0.521	0.052
PonA1	-0.433	0.44
EccD1_KO	0.556	-0.122
EspI_KO	0.114	0.884
PE35_KO	-0.12	0.245
PPE68_KO	-0.266	0.211
glycerol2	0.338	0.821
lignocerate	0.813	0.659
oleate	0.386	0.946
phosphatidylcholine	0.829	0.797
acetate	0.068	-0.145
glucAc	0.289	-0.366
Rv0950ko	0.416	0.603
Rv1096ko	0.329	-0.805
Rv3684ko	0.37	-0.033
delta_otsA_trehalose	-1.403	-0.53