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 Rv1899c/lppD:

update plot	correlation	link to info on gene
Rv2345/-	(cc=0.6084)	info on Rv2345/-
Rv2313c/-	(cc=0.5243)	info on Rv2313c/-
Rv1947/-	(cc=0.5203)	info on Rv1947/-
Rv1970/lprM	(cc=0.5014)	info on Rv1970/lprM
Rv1000c/-	(cc=0.4895)	info on Rv1000c/-
Rv1726/-	(cc=0.4863)	info on Rv1726/-
Rv1997/ctpF	(cc=0.4761)	info on Rv1997/ctpF
Rv2010/vapC15	(cc=0.4723)	info on Rv2010/vapC15
Rv1399c/nlhH	(cc=0.4516)	info on Rv1399c/nlhH
Rv1624c/-	(cc=0.4467)	info on Rv1624c/-

Correlation of Rv1899c/lppD with Rv2345/-

Normalized LFCs for Rv1899c/lppD:
(description and provenance of datasets)

	Rv1899c/lppD	Rv2345/-
Fe_supp_jason_reseq	-0.295	-0.019
low_pH_jason_reseq	-0.371	-0.962
NO_jason_reseq	0.121	-0.053
B6_jason_reseq	-0.499	-0.063
MHCII_jason_reseq	0.088	0.065
Isoniazid02	-1.49	-1.199
Rifampicin4	-0.279	0.509
Ethambutol3	-0.8	-1.019
Meropenem3	-1.127	-1.409
Vancomycin16	-0.809	-0.655
Rv2680_day32	0.228	-0.466
H37Rv_KO_MarP	-0.21	-0.02
hypoxia_3wks	-0.096	0.032
hypoxia_6wks	0.096	0.257
glycerol	0.654	0.192
cholesterol	0.101	-0.086
AJ	-0.079	0.0
Bibs02	-0.383	-0.278
Bibs02c	-0.018	-0.205
BL6	-0.426	0.138
BL6a	-0.211	0.118
BXD01	-0.079	0.14
BXD010	-0.185	0.141
BXD011	-0.209	-0.262
BXD03	-0.542	-0.04
BXD04	-0.191	0.291
BXD05	-0.046	0.374
BXD06	-0.401	0.147
BXD07	-0.276	0.238
BXD08	-0.167	0.434
BXD09	-0.331	0.199
CAST	0.24	-0.225
CCcont	-0.449	0.024
DS01	0.173	0.0
DS02	-0.455	-0.498
DS04	0.358	-0.142
DS0c	-0.055	-0.057
GP01	0.594	0.277
GP02	0.124	0.072
GP0c	0.425	0.147
NOD	-0.218	0.265
NZO	-0.448	-0.237
PWK	-0.59	-0.058
H37Rv_KO_CtpC	0.703	0.373
H37Rv_KO_CtpD	0.221	0.605
H37Rv_KO_Rv1272	0.629	0.291
H37Rv_KO_SugABC	0.582	0.767
H37Rv_KO_MbtN	0.818	0.628
Trans05	0.614	0.501
macrophage_unactivated	0.846	-0.114
IL1	1.51	0.338
Rapamycin	-0.068	0.473
Tcell	0.094	0.039
GMCSF	0.61	0.599
IFNab	0.463	0.311
IFNg	0.019	0.216
IFNg_GMCSF1	0.314	0.182
Rv1432_day32	0.284	0.194
Rv1565c_day32	0.638	0.175
secA2_input	-0.091	0.233
delta_Rv3594	0.185	0.271
delta_Rv3717	-0.174	0.055
delta_Rv3811	0.015	0.352
delta_Rv0954	-0.406	0.371
PonA1	0.495	-0.321
EccD1_KO	0.865	0.704
EspI_KO	0.145	0.767
PE35_KO	0.738	0.429
PPE68_KO	0.825	0.176
glycerol2	-0.014	0.277
lignocerate	-0.128	0.284
oleate	0.295	0.702
phosphatidylcholine	0.157	0.153
acetate	-0.103	-0.462
glucAc	-0.075	-0.232
Rv0950ko	0.066	0.434
Rv1096ko	-0.377	-0.567
Rv3684ko	-0.072	-0.54
delta_otsA_trehalose	0.975	0.582