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 Rv1831/-

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

	Rv2456c/-	Rv1831/-
Fe_supp_jason_reseq	-0.379	-0.275
low_pH_jason_reseq	-1.086	-0.952
NO_jason_reseq	0.0	-0.68
B6_jason_reseq	0.476	-1.36
MHCII_jason_reseq	-0.595	-0.162
Isoniazid02	0.215	0.665
Rifampicin4	0.143	-0.531
Ethambutol3	0.591	1.136
Meropenem3	-0.126	0.271
Vancomycin16	0.048	-0.355
Rv2680_day32	0.302	0.69
H37Rv_KO_MarP	0.071	-0.512
hypoxia_3wks	-0.423	0.124
hypoxia_6wks	0.355	1.021
glycerol	-0.648	-0.11
cholesterol	0.259	0.052
AJ	-0.224	-0.613
Bibs02	-0.301	-1.674
Bibs02c	-0.076	0.349
BL6	0.922	0.796
BL6a	0.716	1.37
BXD01	0.662	2.036
BXD010	0.612	0.407
BXD011	1.502	1.379
BXD03	0.774	1.217
BXD04	1.111	1.986
BXD05	0.484	1.501
BXD06	0.863	1.635
BXD07	0.971	1.565
BXD08	0.717	2.417
BXD09	0.702	1.261
CAST	0.929	-0.087
CCcont	0.332	1.331
DS01	-0.399	-0.349
DS02	0.0	-0.487
DS04	-0.128	1.148
DS0c	0.061	0.476
GP01	0.393	-0.413
GP02	0.291	1.186
GP0c	0.461	-0.086
NOD	0.428	1.302
NZO	0.321	-1.05
PWK	0.186	0.198
H37Rv_KO_CtpC	0.495	0.72
H37Rv_KO_CtpD	-0.268	-0.09
H37Rv_KO_Rv1272	0.562	1.759
H37Rv_KO_SugABC	-0.214	1.836
H37Rv_KO_MbtN	0.886	1.611
Trans05	1.071	1.252
macrophage_unactivated	-0.167	0.568
IL1	0.077	-0.083
Rapamycin	-0.009	-0.439
Tcell	0.502	0.091
GMCSF	0.185	0.314
IFNab	-0.212	0.689
IFNg	0.195	0.265
IFNg_GMCSF1	0.031	0.547
Rv1432_day32	0.149	1.313
Rv1565c_day32	-0.442	-0.471
secA2_input	-0.092	-0.25
delta_Rv3594	0.138	-0.494
delta_Rv3717	0.457	0.323
delta_Rv3811	-0.303	-0.004
delta_Rv0954	-0.521	-0.375
PonA1	-0.433	-1.199
EccD1_KO	0.556	0.96
EspI_KO	0.114	0.414
PE35_KO	-0.12	-0.029
PPE68_KO	-0.266	0.106
glycerol2	0.338	-0.263
lignocerate	0.813	0.145
oleate	0.386	0.424
phosphatidylcholine	0.829	0.326
acetate	0.068	-0.8
glucAc	0.289	-0.318
Rv0950ko	0.416	-0.012
Rv1096ko	0.329	-0.546
Rv3684ko	0.37	-0.193
delta_otsA_trehalose	-1.403	-2.555