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 Rv0069c/sdaA:

update plot	correlation	link to info on gene
Rv0338c/-	(cc=0.7502)	info on Rv0338c/-
Rv0320/-	(cc=0.5463)	info on Rv0320/-
Rv0191/-	(cc=0.4888)	info on Rv0191/-
Rv0373c/-	(cc=0.4568)	info on Rv0373c/-
Rv2189c/-	(cc=0.4479)	info on Rv2189c/-
Rv2715/-	(cc=0.4477)	info on Rv2715/-
Rv3068c/pgmA	(cc=0.4325)	info on Rv3068c/pgmA
Rv2394/ggtB	(cc=0.4302)	info on Rv2394/ggtB
Rv1317c/alkA	(cc=0.4268)	info on Rv1317c/alkA
Rv2073c/-	(cc=0.4251)	info on Rv2073c/-

Correlation of Rv0069c/sdaA with Rv2715/-

Normalized LFCs for Rv0069c/sdaA:
(description and provenance of datasets)

	Rv0069c/sdaA	Rv2715/-
Fe_supp_jason_reseq	0.205	-0.508
low_pH_jason_reseq	-1.367	0.796
NO_jason_reseq	-1.265	-0.646
B6_jason_reseq	-0.208	-0.542
MHCII_jason_reseq	0.127	0.346
Isoniazid02	-0.049	1.224
Rifampicin4	-0.233	-0.504
Ethambutol3	0.627	2.932
Meropenem3	0.278	2.498
Vancomycin16	0.836	0.0
Rv2680_day32	-0.372	-0.73
H37Rv_KO_MarP	0.217	0.223
hypoxia_3wks	-0.319	-0.116
hypoxia_6wks	-0.299	0.175
glycerol	2.392	-0.471
cholesterol	6.0	4.799
AJ	0.187	-0.024
Bibs02	-0.592	-0.223
Bibs02c	0.196	1.516
BL6	0.084	0.26
BL6a	0.307	1.24
BXD01	-0.154	0.314
BXD010	-0.171	1.166
BXD011	0.68	0.642
BXD03	-0.631	0.349
BXD04	-0.425	0.809
BXD05	-0.223	0.369
BXD06	-0.038	0.366
BXD07	-0.207	0.357
BXD08	0.329	0.448
BXD09	0.076	0.788
CAST	-0.976	-0.28
CCcont	0.176	0.348
DS01	-0.279	0.429
DS02	-0.325	0.132
DS04	-1.036	0.682
DS0c	0.363	0.046
GP01	0.265	0.804
GP02	-0.138	0.516
GP0c	0.639	0.387
NOD	-1.596	1.787
NZO	-1.472	-0.964
PWK	0.183	0.158
H37Rv_KO_CtpC	0.213	0.607
H37Rv_KO_CtpD	-1.75	0.185
H37Rv_KO_Rv1272	-0.72	0.558
H37Rv_KO_SugABC	0.94	0.898
H37Rv_KO_MbtN	1.301	1.101
Trans05	-0.5	1.278
macrophage_unactivated	0.18	0.3
IL1	0.383	-0.065
Rapamycin	0.807	0.353
Tcell	0.42	0.176
GMCSF	-0.264	-0.148
IFNab	1.167	-0.133
IFNg	0.249	0.644
IFNg_GMCSF1	-0.512	-0.358
Rv1432_day32	0.415	-0.499
Rv1565c_day32	-0.355	-0.655
secA2_input	1.656	-0.11
delta_Rv3594	-0.783	0.728
delta_Rv3717	-0.2	0.151
delta_Rv3811	0.299	1.169
delta_Rv0954	0.399	0.783
PonA1	0.943	0.386
EccD1_KO	0.802	1.095
EspI_KO	-0.645	0.95
PE35_KO	0.055	1.476
PPE68_KO	0.781	0.784
glycerol2	0.171	-0.476
lignocerate	0.183	0.102
oleate	-0.264	-0.216
phosphatidylcholine	-0.067	0.0
acetate	-0.191	0.206
glucAc	-0.249	0.481
Rv0950ko	0.582	-0.109
Rv1096ko	0.582	-0.145
Rv3684ko	-0.069	-0.318
delta_otsA_trehalose	0.027	0.879