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 Rv1716/-:

update plot	correlation	link to info on gene
Rv1969/mce3D	(cc=0.6313)	info on Rv1969/mce3D
Rv2597/-	(cc=0.6118)	info on Rv2597/-
Rv1945/-	(cc=0.5593)	info on Rv1945/-
Rv1736c/narX	(cc=0.5573)	info on Rv1736c/narX
Rv3635/-	(cc=0.5275)	info on Rv3635/-
Rv0007/-	(cc=0.4685)	info on Rv0007/-
Rv3793/embC	(cc=0.4675)	info on Rv3793/embC
Rv1288/-	(cc=0.4655)	info on Rv1288/-
Rv2171/lppM	(cc=0.4652)	info on Rv2171/lppM
Rv0233/nrdB	(cc=0.4622)	info on Rv0233/nrdB

Correlation of Rv1716/- with Rv3793/embC

Normalized LFCs for Rv1716/-:
(description and provenance of datasets)

	Rv1716/-	Rv3793/embC
Fe_supp_jason_reseq	1.457	0.38
low_pH_jason_reseq	0.207	0.0
NO_jason_reseq	1.118	0.0
B6_jason_reseq	0.688	-0.153
MHCII_jason_reseq	1.549	0.123
Isoniazid02	0.405	0.156
Rifampicin4	-1.059	0.29
Ethambutol3	0.085	0.471
Meropenem3	0.063	-0.138
Vancomycin16	-0.297	0.0
Rv2680_day32	0.038	0.554
H37Rv_KO_MarP	0.306	-0.162
hypoxia_3wks	-0.522	0.0
hypoxia_6wks	0.629	0.194
glycerol	-0.398	-0.202
cholesterol	-0.795	0.0
AJ	-0.161	-0.232
Bibs02	0.74	-0.183
Bibs02c	1.159	-0.209
BL6	-0.71	0.714
BL6a	-0.311	0.346
BXD01	-0.792	0.328
BXD010	-0.943	0.583
BXD011	-0.12	0.412
BXD03	-0.619	1.042
BXD04	-0.386	0.485
BXD05	0.565	0.84
BXD06	-1.012	0.432
BXD07	-0.255	0.865
BXD08	-0.498	0.521
BXD09	0.387	0.639
CAST	-0.362	-0.23
CCcont	-0.877	0.376
DS01	0.436	-0.236
DS02	0.744	0.0
DS04	1.727	0.489
DS0c	-0.099	0.547
GP01	-0.057	-0.099
GP02	0.971	-0.083
GP0c	0.676	0.227
NOD	0.539	-0.225
NZO	-1.095	-0.199
PWK	-0.361	0.0
H37Rv_KO_CtpC	0.206	-0.162
H37Rv_KO_CtpD	-1.637	-0.127
H37Rv_KO_Rv1272	-0.222	-0.141
H37Rv_KO_SugABC	-1.644	0.0
H37Rv_KO_MbtN	0.409	-0.103
Trans05	-0.408	0.119
macrophage_unactivated	0.066	0.0
IL1	-0.472	0.219
Rapamycin	0.893	1.034
Tcell	-0.518	0.241
GMCSF	0.723	0.89
IFNab	-0.067	1.197
IFNg	0.168	0.198
IFNg_GMCSF1	-0.575	0.233
Rv1432_day32	0.094	0.0
Rv1565c_day32	6.0	2.676
secA2_input	-1.586	-0.65
delta_Rv3594	1.323	0.635
delta_Rv3717	0.692	0.0
delta_Rv3811	0.416	0.171
delta_Rv0954	1.225	1.368
PonA1	0.299	0.256
EccD1_KO	-0.829	0.329
EspI_KO	0.354	-0.633
PE35_KO	0.204	-0.312
PPE68_KO	0.093	-0.342
glycerol2	-0.46	0.0
lignocerate	-0.222	0.13
oleate	0.23	-0.537
phosphatidylcholine	0.101	-0.338
acetate	-0.042	-0.191
glucAc	-0.308	0.0
Rv0950ko	0.537	0.971
Rv1096ko	0.76	0.347
Rv3684ko	0.583	0.727
delta_otsA_trehalose	0.533	0.681