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 Rv2403c/lppR:

update plot	correlation	link to info on gene
Rv1267c/embR	(cc=0.4808)	info on Rv1267c/embR
Rv2252/-	(cc=0.4473)	info on Rv2252/-
Rv2133c/-	(cc=0.4156)	info on Rv2133c/-
Rv2587c/secD	(cc=0.3712)	info on Rv2587c/secD
Rv2018/-	(cc=0.3678)	info on Rv2018/-
Rv2851c/-	(cc=0.3531)	info on Rv2851c/-
Rv0727c/fucA	(cc=0.3502)	info on Rv0727c/fucA
Rv2454c/-	(cc=0.3471)	info on Rv2454c/-
Rv0661c/vapC7	(cc=0.3436)	info on Rv0661c/vapC7
Rv0129c/fbpC	(cc=0.3421)	info on Rv0129c/fbpC

Correlation of Rv2403c/lppR with Rv0727c/fucA

Normalized LFCs for Rv2403c/lppR:
(description and provenance of datasets)

	Rv2403c/lppR	Rv0727c/fucA
Fe_supp_jason_reseq	-0.592	-0.758
low_pH_jason_reseq	-3.559	-1.317
NO_jason_reseq	1.727	-0.278
B6_jason_reseq	0.436	-0.494
MHCII_jason_reseq	1.955	-0.013
Isoniazid02	1.586	0.18
Rifampicin4	-2.502	0.858
Ethambutol3	-0.799	0.546
Meropenem3	-1.689	-0.02
Vancomycin16	-0.576	0.35
Rv2680_day32	-0.736	0.879
H37Rv_KO_MarP	0.284	0.161
hypoxia_3wks	-0.056	-0.359
hypoxia_6wks	-0.672	-0.975
glycerol	-1.112	0.635
cholesterol	-0.056	0.237
AJ	0.854	0.802
Bibs02	-1.821	1.245
Bibs02c	0.026	1.047
BL6	-2.152	-0.452
BL6a	0.729	0.851
BXD01	0.095	0.908
BXD010	-0.307	-0.097
BXD011	0.137	-0.048
BXD03	-1.031	-0.157
BXD04	0.529	0.937
BXD05	-0.301	0.435
BXD06	0.328	0.431
BXD07	0.27	0.538
BXD08	-0.016	1.181
BXD09	0.302	0.043
CAST	0.057	-0.397
CCcont	-0.506	-0.028
DS01	0.359	0.732
DS02	1.221	0.761
DS04	0.679	1.549
DS0c	0.053	1.197
GP01	1.638	0.545
GP02	0.979	0.855
GP0c	0.11	0.483
NOD	-1.544	-0.231
NZO	0.786	0.545
PWK	-0.502	-0.024
H37Rv_KO_CtpC	-1.326	0.481
H37Rv_KO_CtpD	-0.645	0.363
H37Rv_KO_Rv1272	0.901	0.512
H37Rv_KO_SugABC	-1.704	-1.504
H37Rv_KO_MbtN	-0.546	-1.202
Trans05	0.979	1.105
macrophage_unactivated	1.3	1.55
IL1	0.243	0.314
Rapamycin	0.043	-0.055
Tcell	0.984	1.013
GMCSF	-0.916	-0.38
IFNab	0.774	-0.435
IFNg	1.042	-0.903
IFNg_GMCSF1	0.459	-0.484
Rv1432_day32	-0.532	0.219
Rv1565c_day32	0.218	0.564
secA2_input	-2.923	-0.714
delta_Rv3594	1.41	0.236
delta_Rv3717	0.746	-0.23
delta_Rv3811	-0.281	-1.017
delta_Rv0954	0.678	0.743
PonA1	-0.394	0.107
EccD1_KO	0.697	0.444
EspI_KO	-0.793	-0.137
PE35_KO	-0.306	-0.344
PPE68_KO	0.534	-0.579
glycerol2	-0.158	0.481
lignocerate	0.93	0.699
oleate	-0.245	0.845
phosphatidylcholine	0.412	0.92
acetate	1.45	0.7
glucAc	0.538	0.616
Rv0950ko	-1.321	-0.063
Rv1096ko	-0.492	0.332
Rv3684ko	0.0	0.514
delta_otsA_trehalose	0.103	0.166