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 Rv2040c/-:

update plot	correlation	link to info on gene
Rv2274c/mazF8	(cc=0.5681)	info on Rv2274c/mazF8
Rv1954A/-	(cc=0.5504)	info on Rv1954A/-
Rv1430/PE16	(cc=0.5072)	info on Rv1430/PE16
Rv1980c/mpt64	(cc=0.5032)	info on Rv1980c/mpt64
Rv1561/vapC11	(cc=0.5004)	info on Rv1561/vapC11
Rv2500c/fadE19	(cc=0.4949)	info on Rv2500c/fadE19
Rv1526c/-	(cc=0.4938)	info on Rv1526c/-
Rv3669/-	(cc=0.4922)	info on Rv3669/-
Rv2481c/-	(cc=0.4885)	info on Rv2481c/-
Rv1896c/-	(cc=0.4875)	info on Rv1896c/-

Correlation of Rv2040c/- with Rv1526c/-

Normalized LFCs for Rv2040c/-:
(description and provenance of datasets)

	Rv2040c/-	Rv1526c/-
Fe_supp_jason_reseq	0.032	0.082
low_pH_jason_reseq	0.291	0.043
NO_jason_reseq	-0.399	0.331
B6_jason_reseq	-0.415	-2.248
MHCII_jason_reseq	-1.451	-1.614
Isoniazid02	-0.255	0.047
Rifampicin4	0.252	-0.325
Ethambutol3	-0.27	-0.212
Meropenem3	-0.266	-0.165
Vancomycin16	0.247	-0.133
Rv2680_day32	0.687	-0.548
H37Rv_KO_MarP	-0.052	1.37
hypoxia_3wks	0.467	-0.558
hypoxia_6wks	-0.065	0.0
glycerol	-0.23	0.243
cholesterol	-0.378	-0.038
AJ	0.513	0.225
Bibs02	-2.245	-0.415
Bibs02c	-1.391	0.344
BL6	1.183	2.032
BL6a	-0.03	1.277
BXD01	0.84	1.115
BXD010	0.656	1.082
BXD011	2.53	2.02
BXD03	0.755	1.063
BXD04	0.091	0.426
BXD05	0.598	1.058
BXD06	0.328	0.967
BXD07	0.042	1.868
BXD08	0.118	0.575
BXD09	0.87	1.249
CAST	-0.425	0.707
CCcont	1.059	1.423
DS01	-1.131	0.633
DS02	-0.792	0.748
DS04	-0.468	0.402
DS0c	-0.247	-0.295
GP01	-0.601	0.727
GP02	-1.109	1.017
GP0c	-0.865	1.754
NOD	0.76	1.154
NZO	-0.727	0.1
PWK	0.06	-0.156
H37Rv_KO_CtpC	0.567	1.462
H37Rv_KO_CtpD	0.039	1.973
H37Rv_KO_Rv1272	1.84	2.07
H37Rv_KO_SugABC	-0.918	1.981
H37Rv_KO_MbtN	-0.421	0.479
Trans05	1.52	1.657
macrophage_unactivated	0.325	0.71
IL1	0.089	0.095
Rapamycin	-0.046	0.648
Tcell	0.147	0.909
GMCSF	0.729	0.594
IFNab	0.091	0.239
IFNg	-0.385	1.056
IFNg_GMCSF1	0.826	0.05
Rv1432_day32	-0.415	-0.87
Rv1565c_day32	-0.584	-0.291
secA2_input	-2.616	-0.482
delta_Rv3594	0.352	0.895
delta_Rv3717	0.044	0.029
delta_Rv3811	0.696	1.17
delta_Rv0954	-0.439	0.652
PonA1	0.212	1.392
EccD1_KO	0.605	0.835
EspI_KO	0.727	0.967
PE35_KO	1.164	0.989
PPE68_KO	1.072	0.95
glycerol2	-0.273	0.376
lignocerate	0.012	1.333
oleate	-0.597	-1.157
phosphatidylcholine	0.193	0.758
acetate	-0.032	1.403
glucAc	0.105	1.533
Rv0950ko	-0.645	-0.265
Rv1096ko	-1.23	-0.407
Rv3684ko	-2.021	-0.704
delta_otsA_trehalose	-0.103	1.158