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 Rv0188/-

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

	Rv2456c/-	Rv0188/-
Fe_supp_jason_reseq	-0.379	-0.766
low_pH_jason_reseq	-1.086	0.268
NO_jason_reseq	0.0	0.801
B6_jason_reseq	0.476	-0.538
MHCII_jason_reseq	-0.595	0.058
Isoniazid02	0.215	-0.412
Rifampicin4	0.143	0.211
Ethambutol3	0.591	-0.218
Meropenem3	-0.126	0.793
Vancomycin16	0.048	-0.167
Rv2680_day32	0.302	-0.618
H37Rv_KO_MarP	0.071	0.452
hypoxia_3wks	-0.423	-0.291
hypoxia_6wks	0.355	-0.311
glycerol	-0.648	-1.26
cholesterol	0.259	-1.501
AJ	-0.224	-0.548
Bibs02	-0.301	-1.481
Bibs02c	-0.076	-0.862
BL6	0.922	1.733
BL6a	0.716	0.862
BXD01	0.662	1.395
BXD010	0.612	1.117
BXD011	1.502	0.854
BXD03	0.774	0.881
BXD04	1.111	1.39
BXD05	0.484	1.424
BXD06	0.863	1.469
BXD07	0.971	1.263
BXD08	0.717	2.603
BXD09	0.702	1.275
CAST	0.929	0.257
CCcont	0.332	1.593
DS01	-0.399	-0.263
DS02	0.0	-0.75
DS04	-0.128	0.045
DS0c	0.061	-1.307
GP01	0.393	1.934
GP02	0.291	-0.574
GP0c	0.461	0.225
NOD	0.428	-0.107
NZO	0.321	0.285
PWK	0.186	-0.27
H37Rv_KO_CtpC	0.495	-0.078
H37Rv_KO_CtpD	-0.268	-0.994
H37Rv_KO_Rv1272	0.562	0.828
H37Rv_KO_SugABC	-0.214	0.735
H37Rv_KO_MbtN	0.886	1.059
Trans05	1.071	1.637
macrophage_unactivated	-0.167	0.739
IL1	0.077	-0.896
Rapamycin	-0.009	-0.724
Tcell	0.502	-0.368
GMCSF	0.185	0.364
IFNab	-0.212	-0.054
IFNg	0.195	-0.746
IFNg_GMCSF1	0.031	0.195
Rv1432_day32	0.149	-0.026
Rv1565c_day32	-0.442	-0.494
secA2_input	-0.092	-0.43
delta_Rv3594	0.138	-1.205
delta_Rv3717	0.457	-0.76
delta_Rv3811	-0.303	-0.848
delta_Rv0954	-0.521	-0.665
PonA1	-0.433	-1.947
EccD1_KO	0.556	0.569
EspI_KO	0.114	-0.394
PE35_KO	-0.12	-0.21
PPE68_KO	-0.266	0.793
glycerol2	0.338	0.879
lignocerate	0.813	0.693
oleate	0.386	0.549
phosphatidylcholine	0.829	0.704
acetate	0.068	0.411
glucAc	0.289	-0.008
Rv0950ko	0.416	0.09
Rv1096ko	0.329	1.191
Rv3684ko	0.37	1.192
delta_otsA_trehalose	-1.403	-0.811