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 Rv3022A/PE29:

update plot	correlation	link to info on gene
Rv2543/lppA	(cc=0.5866)	info on Rv2543/lppA
Rv1396c/PE_PGRS25	(cc=0.548)	info on Rv1396c/PE_PGRS25
Rv0526/-	(cc=0.5258)	info on Rv0526/-
Rv2519/PE26	(cc=0.5243)	info on Rv2519/PE26
Rv1173/fbiC	(cc=0.5135)	info on Rv1173/fbiC
Rv2807/-	(cc=0.5131)	info on Rv2807/-
Rv1067c/PE_PGRS19	(cc=0.5123)	info on Rv1067c/PE_PGRS19
Rv1918c/PPE35	(cc=0.5079)	info on Rv1918c/PPE35
Rv3023c/-	(cc=0.5041)	info on Rv3023c/-
Rv1047/-	(cc=0.5)	info on Rv1047/-

Correlation of Rv3022A/PE29 with Rv2807/-

Normalized LFCs for Rv3022A/PE29:
(description and provenance of datasets)

	Rv3022A/PE29	Rv2807/-
Fe_supp_jason_reseq	0.275	-0.144
low_pH_jason_reseq	-0.381	-0.033
NO_jason_reseq	-0.709	0.294
B6_jason_reseq	-0.585	-1.393
MHCII_jason_reseq	-0.709	-0.457
Isoniazid02	0.994	-0.937
Rifampicin4	0.967	-1.113
Ethambutol3	0.434	-0.028
Meropenem3	0.291	-0.686
Vancomycin16	0.594	-0.318
Rv2680_day32	-0.826	1.111
H37Rv_KO_MarP	0.165	0.429
hypoxia_3wks	0.347	-0.359
hypoxia_6wks	-0.81	-0.495
glycerol	0.73	-0.282
cholesterol	1.146	0.321
AJ	2.274	-0.363
Bibs02	0.167	0.362
Bibs02c	0.893	1.188
BL6	0.569	0.668
BL6a	0.641	0.987
BXD01	0.898	0.761
BXD010	0.456	0.661
BXD011	0.286	-0.137
BXD03	0.216	0.076
BXD04	0.063	0.087
BXD05	0.775	0.039
BXD06	0.593	0.057
BXD07	0.93	0.505
BXD08	0.28	0.564
BXD09	0.383	0.02
CAST	1.099	0.284
CCcont	1.022	0.757
DS01	0.883	-0.07
DS02	0.745	1.254
DS04	0.748	0.562
DS0c	-0.019	1.196
GP01	0.72	0.85
GP02	0.311	-0.389
GP0c	0.208	0.391
NOD	0.919	-0.169
NZO	-0.088	-0.487
PWK	0.494	-0.443
H37Rv_KO_CtpC	1.553	1.312
H37Rv_KO_CtpD	1.287	1.175
H37Rv_KO_Rv1272	2.221	1.986
H37Rv_KO_SugABC	0.898	1.246
H37Rv_KO_MbtN	0.687	1.011
Trans05	1.378	0.274
macrophage_unactivated	0.767	-0.322
IL1	0.039	-0.356
Rapamycin	0.264	-0.206
Tcell	0.525	-1.212
GMCSF	1.333	0.169
IFNab	0.768	-0.698
IFNg	0.083	-0.567
IFNg_GMCSF1	0.289	-0.104
Rv1432_day32	0.85	0.112
Rv1565c_day32	2.139	-0.193
secA2_input	0.182	-1.518
delta_Rv3594	0.34	-0.82
delta_Rv3717	0.145	-1.514
delta_Rv3811	0.427	-0.754
delta_Rv0954	-0.225	-0.91
PonA1	0.516	-1.415
EccD1_KO	0.947	1.181
EspI_KO	1.178	1.358
PE35_KO	0.84	0.435
PPE68_KO	0.579	1.225
glycerol2	-1.302	-1.701
lignocerate	-0.961	-0.955
oleate	-1.032	-2.164
phosphatidylcholine	-0.819	-1.364
acetate	-1.248	-1.647
glucAc	-0.722	-0.036
Rv0950ko	0.555	-0.642
Rv1096ko	-0.347	0.0
Rv3684ko	-0.354	0.331
delta_otsA_trehalose	-1.531	-1.844