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 Rv3487c/lipF:

update plot	correlation	link to info on gene
Rv3425/PPE57	(cc=0.5702)	info on Rv3425/PPE57
Rv0072/-	(cc=0.5657)	info on Rv0072/-
Rv3840/-	(cc=0.552)	info on Rv3840/-
Rv2443/dctA	(cc=0.5494)	info on Rv2443/dctA
Rv1386/PE15	(cc=0.5433)	info on Rv1386/PE15
Rv3784/-	(cc=0.5374)	info on Rv3784/-
Rv1509/-	(cc=0.5351)	info on Rv1509/-
Rv1831/-	(cc=0.5211)	info on Rv1831/-
Rv1787/PPE25	(cc=0.5186)	info on Rv1787/PPE25
Rv2430c/PPE41	(cc=0.5167)	info on Rv2430c/PPE41

Correlation of Rv3487c/lipF with Rv2443/dctA

Normalized LFCs for Rv3487c/lipF:
(description and provenance of datasets)

	Rv3487c/lipF	Rv2443/dctA
Fe_supp_jason_reseq	-0.019	-0.074
low_pH_jason_reseq	-1.251	-1.052
NO_jason_reseq	-0.239	-0.108
B6_jason_reseq	-0.625	-0.548
MHCII_jason_reseq	-0.39	-0.268
Isoniazid02	0.253	-0.426
Rifampicin4	0.084	0.049
Ethambutol3	0.445	-0.383
Meropenem3	-0.216	0.152
Vancomycin16	-0.151	-0.501
Rv2680_day32	-0.366	0.053
H37Rv_KO_MarP	0.374	-0.121
hypoxia_3wks	0.072	-0.068
hypoxia_6wks	0.58	0.267
glycerol	-0.127	-0.601
cholesterol	-0.321	0.37
AJ	0.242	0.977
Bibs02	0.181	0.424
Bibs02c	-0.299	-0.238
BL6	0.189	0.607
BL6a	0.083	0.026
BXD01	0.158	0.443
BXD010	0.391	0.305
BXD011	0.364	0.372
BXD03	0.223	0.386
BXD04	0.761	0.409
BXD05	0.801	0.023
BXD06	0.025	0.535
BXD07	0.311	0.444
BXD08	0.615	0.468
BXD09	0.034	0.321
CAST	0.457	0.469
CCcont	0.187	-0.236
DS01	0.031	0.224
DS02	-0.447	0.224
DS04	0.777	0.707
DS0c	-0.676	0.127
GP01	0.17	0.029
GP02	1.009	1.221
GP0c	-0.039	-0.023
NOD	0.703	0.926
NZO	-0.143	0.433
PWK	0.595	1.698
H37Rv_KO_CtpC	0.674	0.021
H37Rv_KO_CtpD	0.353	0.851
H37Rv_KO_Rv1272	0.153	0.262
H37Rv_KO_SugABC	0.648	0.711
H37Rv_KO_MbtN	0.375	0.026
Trans05	0.556	-0.081
macrophage_unactivated	0.256	0.347
IL1	-0.059	-0.492
Rapamycin	-0.031	-0.488
Tcell	0.042	-0.14
GMCSF	-0.209	0.127
IFNab	-0.082	-0.166
IFNg	0.462	0.556
IFNg_GMCSF1	0.163	0.892
Rv1432_day32	0.808	0.262
Rv1565c_day32	0.419	0.889
secA2_input	0.122	-0.728
delta_Rv3594	-0.378	-0.486
delta_Rv3717	-0.602	-0.79
delta_Rv3811	-0.47	-0.431
delta_Rv0954	-0.77	0.481
PonA1	-0.34	0.369
EccD1_KO	-0.118	-0.332
EspI_KO	-0.262	-0.599
PE35_KO	-1.105	-0.551
PPE68_KO	-0.752	-0.787
glycerol2	0.604	0.067
lignocerate	0.57	-0.03
oleate	0.693	0.492
phosphatidylcholine	0.787	0.242
acetate	-0.274	-0.258
glucAc	0.247	-0.762
Rv0950ko	0.374	-0.25
Rv1096ko	-0.543	-0.835
Rv3684ko	-1.123	-0.698
delta_otsA_trehalose	-0.799	0.483