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 Rv3068c/pgmA:
Show top 50 genes. Show bottom 10 genes with LOWEST correlation.

Most correlated genes.

update plot	correlation	link to info on gene
Rv1178/-	(cc=0.4906)	info on Rv1178/-
Rv0003/recF	(cc=0.486)	info on Rv0003/recF
Rv3624c/hpt	(cc=0.4806)	info on Rv3624c/hpt
Rv3262/fbiB	(cc=0.4732)	info on Rv3262/fbiB
Rv3433c/-	(cc=0.4632)	info on Rv3433c/-
Rv3855/ethR	(cc=0.461)	info on Rv3855/ethR
Rv0338c/-	(cc=0.4596)	info on Rv0338c/-
Rv1020/mfd	(cc=0.4543)	info on Rv1020/mfd
Rv1422/-	(cc=0.4387)	info on Rv1422/-
Rv1633/uvrB	(cc=0.4382)	info on Rv1633/uvrB

Correlation of Rv3068c/pgmA with Rv1178/-

Normalized LFCs for Rv3068c/pgmA:
(description and provenance of datasets)

Comparison of LFCs between selected condtions.

condition	Rv3068c/pgmA	Rv1178/-
Fe_supp_jason_reseq	-0.557	-1.039
low_pH_jason_reseq	-1.005	0.527
NO_jason_reseq	-0.927	-5.222
B6_jason_reseq	0.188	-1.36
MHCII_jason_reseq	-0.345	-2.581
Isoniazid02	-0.185	-1.072
Rifampicin4	-0.236	-0.523
Ethambutol3	0.1	1.677
Meropenem3	0.365	1.154
Vancomycin16	0.127	-0.976
Rv2680_day32	0.223	-2.122
H37Rv_KO_MarP	0.058	3.838
hypoxia_3wks	-2.731	-4.625
hypoxia_6wks	-3.408	-2.422
glycerol	-0.14	1.631
cholesterol	3.524	1.675
AJ	-0.21	-0.585
Bibs02	-0.619	-0.294
Bibs02c	-0.483	-0.277
BL6	0.179	-0.53
BL6a	0.056	0.049
BXD01	0.261	-0.458
BXD010	0.242	-0.065
BXD011	0.659	-0.243
BXD03	0.39	-0.573
BXD04	0.157	0.117
BXD05	0.455	-0.975
BXD06	0.289	-0.337
BXD07	0.188	0.034
BXD08	-0.127	-0.422
BXD09	0.072	-0.494
CAST	-0.27	-0.654
CCcont	-0.128	1.517
DS01	-0.152	-0.83
DS02	0.082	-0.288
DS04	0.495	0.0
DS0c	-0.338	-1.268
GP01	1.364	-0.382
GP02	0.758	-0.839
GP0c	0.159	-0.551
NOD	-0.898	-0.789
NZO	-0.244	0.405
PWK	-0.057	-1.326
H37Rv_KO_CtpC	0.069	0.329
H37Rv_KO_CtpD	-0.262	0.061
H37Rv_KO_Rv1272	-0.142	-0.109
H37Rv_KO_SugABC	0.48	0.138
H37Rv_KO_MbtN	-0.62	-0.558
Trans05	-0.416	0.0
macrophage_unactivated	0.202	0.609
IL1	-0.288	0.463
Rapamycin	-0.347	1.114
Tcell	-0.094	0.388
GMCSF	0.349	-1.436
IFNab	-0.088	-1.297
IFNg	-0.388	-1.0
IFNg_GMCSF1	0.069	0.49
Rv1432_day32	0.576	-1.602
Rv1565c_day32	-0.444	-3.533
secA2_input	0.095	-0.205
delta_Rv3594	-0.075	-0.199
delta_Rv3717	-0.43	-1.602
delta_Rv3811	-0.65	-1.344
delta_Rv0954	-0.208	2.212
PonA1	0.167	1.711
EccD1_KO	0.431	0.47
EspI_KO	0.374	0.485
PE35_KO	-0.257	0.723
PPE68_KO	-0.55	0.873
glycerol2	0.269	-1.789
lignocerate	-2.53	-2.153
oleate	-2.101	-2.105
phosphatidylcholine	-3.003	-2.899
acetate	0.229	-0.888
glucAc	-0.089	-0.754
Rv0950ko	0.419	3.745
Rv1096ko	0.709	2.569
Rv3684ko	0.563	3.871
delta_otsA_trehalose	0.3	0.415