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 Rv2851c/-

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

	Rv2403c/lppR	Rv2851c/-
Fe_supp_jason_reseq	-0.592	-0.021
low_pH_jason_reseq	-3.559	-0.852
NO_jason_reseq	1.727	2.539
B6_jason_reseq	0.436	0.843
MHCII_jason_reseq	1.955	1.51
Isoniazid02	1.586	0.781
Rifampicin4	-2.502	-0.319
Ethambutol3	-0.799	0.14
Meropenem3	-1.689	0.478
Vancomycin16	-0.576	-0.653
Rv2680_day32	-0.736	1.779
H37Rv_KO_MarP	0.284	0.562
hypoxia_3wks	-0.056	0.809
hypoxia_6wks	-0.672	0.472
glycerol	-1.112	0.884
cholesterol	-0.056	-1.323
AJ	0.854	-0.484
Bibs02	-1.821	0.0
Bibs02c	0.026	-0.217
BL6	-2.152	0.463
BL6a	0.729	0.08
BXD01	0.095	0.373
BXD010	-0.307	0.052
BXD011	0.137	0.149
BXD03	-1.031	-0.99
BXD04	0.529	0.744
BXD05	-0.301	0.514
BXD06	0.328	-0.091
BXD07	0.27	-0.131
BXD08	-0.016	0.589
BXD09	0.302	1.403
CAST	0.057	-1.333
CCcont	-0.506	0.612
DS01	0.359	-0.517
DS02	1.221	1.549
DS04	0.679	-0.632
DS0c	0.053	0.635
GP01	1.638	2.288
GP02	0.979	0.201
GP0c	0.11	1.225
NOD	-1.544	-0.835
NZO	0.786	0.533
PWK	-0.502	-0.776
H37Rv_KO_CtpC	-1.326	0.248
H37Rv_KO_CtpD	-0.645	0.484
H37Rv_KO_Rv1272	0.901	0.609
H37Rv_KO_SugABC	-1.704	2.202
H37Rv_KO_MbtN	-0.546	1.314
Trans05	0.979	1.236
macrophage_unactivated	1.3	0.956
IL1	0.243	1.777
Rapamycin	0.043	2.55
Tcell	0.984	1.033
GMCSF	-0.916	1.067
IFNab	0.774	0.051
IFNg	1.042	3.814
IFNg_GMCSF1	0.459	4.286
Rv1432_day32	-0.532	1.601
Rv1565c_day32	0.218	-0.31
secA2_input	-2.923	-0.56
delta_Rv3594	1.41	0.716
delta_Rv3717	0.746	0.405
delta_Rv3811	-0.281	0.882
delta_Rv0954	0.678	0.031
PonA1	-0.394	-1.27
EccD1_KO	0.697	0.789
EspI_KO	-0.793	0.819
PE35_KO	-0.306	0.289
PPE68_KO	0.534	0.451
glycerol2	-0.158	3.544
lignocerate	0.93	3.187
oleate	-0.245	-1.418
phosphatidylcholine	0.412	3.27
acetate	1.45	2.809
glucAc	0.538	2.649
Rv0950ko	-1.321	0.585
Rv1096ko	-0.492	0.558
Rv3684ko	0.0	1.041
delta_otsA_trehalose	0.103	2.311