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 Rv1267c/embR

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

	Rv2403c/lppR	Rv1267c/embR
Fe_supp_jason_reseq	-0.592	-0.406
low_pH_jason_reseq	-3.559	-0.234
NO_jason_reseq	1.727	0.184
B6_jason_reseq	0.436	0.172
MHCII_jason_reseq	1.955	1.059
Isoniazid02	1.586	-0.367
Rifampicin4	-2.502	-0.06
Ethambutol3	-0.799	-0.291
Meropenem3	-1.689	-0.195
Vancomycin16	-0.576	-0.369
Rv2680_day32	-0.736	-0.344
H37Rv_KO_MarP	0.284	0.683
hypoxia_3wks	-0.056	-0.566
hypoxia_6wks	-0.672	-0.679
glycerol	-1.112	-0.199
cholesterol	-0.056	-0.3
AJ	0.854	0.449
Bibs02	-1.821	0.045
Bibs02c	0.026	0.917
BL6	-2.152	-0.098
BL6a	0.729	0.58
BXD01	0.095	-0.084
BXD010	-0.307	0.1
BXD011	0.137	0.1
BXD03	-1.031	-0.725
BXD04	0.529	0.77
BXD05	-0.301	-0.453
BXD06	0.328	-0.077
BXD07	0.27	0.365
BXD08	-0.016	-0.113
BXD09	0.302	0.242
CAST	0.057	0.652
CCcont	-0.506	-0.221
DS01	0.359	0.13
DS02	1.221	-0.041
DS04	0.679	0.446
DS0c	0.053	0.207
GP01	1.638	1.658
GP02	0.979	2.343
GP0c	0.11	1.044
NOD	-1.544	0.812
NZO	0.786	0.555
PWK	-0.502	0.35
H37Rv_KO_CtpC	-1.326	-0.386
H37Rv_KO_CtpD	-0.645	-0.272
H37Rv_KO_Rv1272	0.901	0.808
H37Rv_KO_SugABC	-1.704	-0.342
H37Rv_KO_MbtN	-0.546	-0.102
Trans05	0.979	0.54
macrophage_unactivated	1.3	0.395
IL1	0.243	0.486
Rapamycin	0.043	0.068
Tcell	0.984	0.984
GMCSF	-0.916	-0.235
IFNab	0.774	-0.828
IFNg	1.042	0.946
IFNg_GMCSF1	0.459	0.694
Rv1432_day32	-0.532	0.188
Rv1565c_day32	0.218	0.292
secA2_input	-2.923	-0.2
delta_Rv3594	1.41	0.792
delta_Rv3717	0.746	0.944
delta_Rv3811	-0.281	0.208
delta_Rv0954	0.678	0.699
PonA1	-0.394	0.278
EccD1_KO	0.697	1.125
EspI_KO	-0.793	0.388
PE35_KO	-0.306	1.03
PPE68_KO	0.534	0.518
glycerol2	-0.158	0.273
lignocerate	0.93	0.581
oleate	-0.245	0.33
phosphatidylcholine	0.412	0.545
acetate	1.45	0.51
glucAc	0.538	0.045
Rv0950ko	-1.321	0.308
Rv1096ko	-0.492	0.715
Rv3684ko	0.0	0.475
delta_otsA_trehalose	0.103	0.858